Error in read.table

[dashainparis]

Hello that it is me again! Thank you for the previous answer!

I have another question, I ran ExomeDel on my data and keep getting this error:

Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.bigFile -> read.delim -> read.table
Execution halted

I definitely have a file to read it, I really do not get what am I doing wrong.

Thank you in advance!

Dasha

[dashainparis]

Ok, I think I found what is the error.

In readme for the gtf file you ask the following format:

#gtf file:
#Column1 ... Column3 Column4 Column5 ...
Chromosome ... exon StartPosition EndPosition ...

but actually in example folder for gtf file you have this format:

#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames

and the code is written for the the second format, so the classical gtf file does not suit it.

Am I missing something, may be I should gtf download from somewhere else?

Thank you in advance!

Dasha

[pineapple216]

I experience the same error. @dashainparis did you had any success trying to run the program with a differently formatted gtf file as you suggested above?

UPDATE: I've tried to run ExonDel with a differently formatted .gtf file and I still get the same error.

[dashainparis]

Well, actually I did not succeeded to get to the end, but I had different type of error and I guess it is in my bam files.

I am not sure where can be downloaded exactly this format, but thought the uscs you can get this:

#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinID alignID

I added the first column #bin just manually something like 0 everywhere (I've checked it is not used in the code).

[pineapple216]

I've run the program with a gtf file formatted the same as in the example and I get the same error.
The file I used as gtf file can be found here:

https://www.dropbox.com/s/59n4q8evtqwaicz/refGene.hg19.24feb2015ucsc.txt?dl=0

[dashainparis]

Thanks! Then I actually do not know, because it worked for me. But perl code is well written and very readable (well as it could be for perl), so good luck!

[pineapple216]

@dashainparis Did you manage to get it working?

[slzhao]

Hello Dasha and Koen,

You are right. The format of gft file in README is not correct. It was
copied from my another software and was not for ExonDel. The format of
example gtf file is correct. I will change the README file soon.

For the gtf files, You can download it from UCSC (
http://genome.ucsc.edu/cgi-bin/hgTables), and select track as RefSeq Genes.
The file can be used in ExonDel.

To Koen:
For the error message, it happened when reading files into R and I am not
sure if it was related with the gtf format.
I will fix it If you can send part of the files ("genesPassQCwithGC.bed"
and "genesPassQCwithGC.bed.depth") to me.

Thank you!

Best,
Shilin

2015-03-25 9:32 GMT-05:00 Dasha notifications@github.com:

Thanks! Then I actually do not know, because it worked for me. But perl
code is well written and very readable (well as it could be for perl), so
good luck!

—
Reply to this email directly or view it on GitHub
#2 (comment).

[pineapple216]

Dear Shilin,

I've checked the files you mentioned.

"genesPassQCwithGC.bed" is empty and "genesPassQCwithGC.bed.depth" contains the following:

DNA03-03099-BRCA1
DNA04-04960-BRCA1
DNA05-02178-BRCA1
DNA05-02206-BRCA1
DNA07-07992-BRCA1
DNA07-09019-BRCA1
DNA07-10821-BRCA1
DNA08-04752-BRCA1
DNA08-07116-BRCA1
DNA09-03624A-BRCA1
DNA09-08514-BRCA1
DNA09-13320A-BRCA1
DNA09-14933A-BRCA1

These are the sample names in my case.

Koen

[dashainparis]

Dear Shilin,

Thank you for the answer.

I actually managed to run the tool, but I had several obstacles on my way.

First is due the chromosomes names. Actually if you work with any human data you will have chr in the chromosome names, and at the same time you always have just number in other files, so easier you manually change all you data (which is a lot, and also it ruins other tools workflow), easier you change the code.

And second thing which took me a while to catch. Is that in bamList it is very strict according to the number of tubs. So I had two and it did not work at all.

But after all tool seems to work really good with my data, thank you for it!

Dasha

[pineapple216]

Dear Shilin,

Do you have an estimation how much time it will take to fix ExonDel?

Kind regards,

Koen Hendriks

[slzhao]

Hello Dasha,

For the first thing, do you mean I can change the code so that it can be
used for both chromosome "chr1" and "1"? Such kind of code exists for all
annotation files including gtf and bed, but I didn't add them to bam file
processing because that would be slow. I will add them to bam processing in
next version.
For the second thing, do you mean columns? You can only have bam file names
in the bam list file. which is only one column.

Please let me know if you have other questions.

Best,
Shilin

2015-03-30 3:43 GMT-05:00 Dasha notifications@github.com:

Dear Shilin,

Thank you for the answer.

I actually managed to run the tool, but I had several obstacles on my way.

First is due the chromosomes names. Actually if you work with any human
data you will have chr in the chromosome names, and at the same time you
always have just number in other files, so easier you manually change all
you data (which is a lot, and also it ruins other tools workflow), easier
you change the code.

And second thing which took me a while to catch. Is that in bamList it is
very strict according to the number of tubs. So I had two and it did not
work at all.

But after all tool seems to work really good with my data, thank you for
it!

Dasha

—
Reply to this email directly or view it on GitHub
#2 (comment).

[slzhao]

Hello Koen,

What about the genesPassQC.bed and covered_percentage file? Can you send me
part of them if they are not empty. I need to see some result files to know
how to fix it.

Best,
Shilin

2015-04-02 3:36 GMT-05:00 Koen Hendriks notifications@github.com:

Dear Shilin,

Do you have an estimation how much time it will take to fix ExonDel?

Kind regards,

Koen Hendriks

—
Reply to this email directly or view it on GitHub
#2 (comment).

[pineapple216]

Hello Shilin,

I've run ExonDel again and this is in my covered_percentage file:

#bin name om strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames coveredBP coveredExon
19 NM_001291929 11 - 89057521 89223909 89059923 89223852 17 89057521,89069012,89070614,89073230,89075241,89088129,89106599,89133184,89133382,89135493,89155069,89165951,89173855,89177302,89182607,89184952,89223774, 89060044,89069113,89070683,89073339,89075361,89088211,89106660,89133247,89133547,89135710,89155150,89166024,89173883,89177400,89182692,89185063,89223909, 0 NOX4 cmpl cmpl 2,0,0,2,2,1,0,0,0,2,2,1,0,1,0,0,0, 0.400434992750121 0.882352941176471
985 NM_016039 14 + 52456227 52471420 52456357 52471234 8 52456227,52458034,52460440,52465211,52466425,52468515,52470911,52471079, 52456418,52458159,52460540,52465298,52466514,52468584,52470960,52471420, 0 C14orf166 cmpl cmpl 0,1,0,1,1,0,0,1, 0.768649669499528 1
858 NM_006739 22 + 35796115 35820495 35796431 35820248 17 35796115,35796423,35799199,35799406,35802545,35804400,35806736,35808502,35809867,35811821,35812331,35812630,35813736,35815876,35817310,35819206,35820146, 35796201,35796598,35799326,35799535,35802718,35804556,35806903,35808674,35809979,35811965,35812397,35812807,35813849,35816005,35817453,35819334,35820495, 0 MCM5 cmpl cmpl -1,0,2,0,0,2,2,1,2,0,0,0,0,2,2,1,0, 0.873195474053843 0.941176470588235
1761 NM_032385 5 - 154198051 154230213 154199875 154217738 9 154198051,154200819,154202031,154202946,154210360,154214184,154214402,154217690,154230042, 154200032,154200986,154202137,154203152,154210482,154214288,154214494,154217738,154230213, 0 FAXDC2 cmpl cmpl 2,0,2,0,1,2,0,0,-1, 0.349634065202928 0.888888888888889
587 NM_021034 11 - 319672 320914 319837 320813 2 319672,320564, 319990,320914, 0 IFITM3 cmpl cmpl 0,0, 0.749253731343284 1
1162 NM_020932 X + 75648045 75651746 75648323 75651197 1 75648045, 75651746, 0 MAGEE1 cmpl cmpl 0, 0.809832522960562 1
13 NM_020929 11 - 40135750 41481186 40135919 40137842 5 40135750,40162350,40341177,40669691,41480980, 40137884,40162403,40341271,40669828,41481186, 0 LRRC4C cmpl cmpl 0,-1,-1,-1,-1, 0.769874476987448 0.2
1352 NM_021029 X + 100645877 100651142 100645923 100650736 5 100645877,100646446,100646742,100650322,100650715, 100646034,100646552,100646810,100650445,100651142, 0 RPL36A cmpl cmpl 0,0,1,0,0, 0.488713318284424 1
1688 NM_032378 8 - 144661866 144679845 144661961 144672251 10 144661866,144662181,144662675,144663223,144663398,144668388,144668898,144671160,144672777,144679517, 144662000,144662376,144662897,144663324,144663498,144668460,144669022,144672251,144672908,144679845, 0 EEF1D cmpl cmpl 0,0,0,1,0,0,2,0,-1,-1, 0.80622009569378 0.8
106 NR_002833 7 - 35120898 35225774 35225774 35225774 22

genesPassQC.bed contains the following±

14 52456227 52456418 C14orf166 NM_016039
14 52458034 52458159 C14orf166 NM_016039
14 52460440 52460540 C14orf166 NM_016039
14 52465211 52465298 C14orf166 NM_016039
14 52466425 52466514 C14orf166 NM_016039
14 52468515 52468584 C14orf166 NM_016039
14 52470911 52470960 C14orf166 NM_016039
14 52471079 52471420 C14orf166 NM_016039
11 319672 319990 IFITM3 NM_021034
11 320564 320914 IFITM3 NM_021034
X 75648045 75651746 MAGEE1 NM_020932
X 100645877 100646034 RPL36A NM_021029
X 100646446 100646552 RPL36A NM_021029
X 100646742 100646810 RPL36A NM_021029
X 100650322 100650445 RPL36A NM_021029
X 100650715 100651142 RPL36A NM_021029
19 48373722 48374824 SULT2A1 NM_003167
19 48377913 48378091 SULT2A1 NM_003167
19 48382292 48382387 SULT2A1 NM_003167
19 48385340 48385467 SULT2A1 NM_003167
19 48386833 48387042 SULT2A1 NM_003167
19 48389378 48389654 SULT2A1 NM_003167
1 26856248 26856474 RPS6KA1 NM_002953
1 26863415 26863460 RPS6KA1 NM_002953
1 26873357 26873474 RPS6KA1 NM_002953
1 26873679 26873761 RPS6KA1 NM_002953
1 26877887 26877968 RPS6KA1 NM_002953
1 26878134 26878214 RPS6KA1 NM_002953
1 26879881 26879988 RPS6KA1 NM_002953
1 26880704 26880742 RPS6KA1 NM_002953
1 26881086 26881229 RPS6KA1 NM_002953
1 26881641 26881712 RPS6KA1 NM_002953
1 26882027 26882116 RPS6KA1 NM_002953
1 26883144 26883209 RPS6KA1 NM_002953
1 26883488 26883591 RPS6KA1 NM_002953
1 26885297 26885428 RPS6KA1 NM_002953
1 26887216 26887342 RPS6KA1 NM_002953
1 26887535 26887625 RPS6KA1 NM_002953
1 26887995 26888154 RPS6KA1 NM_002953
1 26897939 26898101 RPS6KA1 NM_002953
1 26898339 26898416 RPS6KA1 NM_002953
1 26898666 26898784 RPS6KA1 NM_002953
1 26899714 26899852 RPS6KA1 NM_002953
1 26900569 26901520 RPS6KA1 NM_002953
20 36932551 36932755 BPI NM_001725
20 36935968 36936083 BPI NM_001725
20 36937331 36937460 BPI NM_001725
20 36938892 36939054 BPI NM_001725
20 36940275 36940339 BPI NM_001725
20 36946814 36946878 BPI NM_001725
20 36948584 36948676 BPI NM_001725
20 36952271 36952448 BPI NM_001725
20 36953175 36953235 BPI NM_001725
20 36954666 36954834 BPI NM_001725
20 36955989 36956057 BPI NM_001725
20 36959449 36959492 BPI NM_001725
20 36962831 36962895 BPI NM_001725
20 36963999 36964076 BPI NM_001725
20 36965547 36965905 BPI NM_001725
16 11361713 11361869 TNP2 NM_005425
16 11362719 11363160 TNP2 NM_005425
11 120973374 120973438 TECTA NM_005422
11 120976539 120976673 TECTA NM_005422
11 120979919 120980207 TECTA NM_005422
11 120983780 120983918 TECTA NM_005422
11 120984261 120984427 TECTA NM_005422
11 120989014 120989427 TECTA NM_005422
11 120996010 120996581 TECTA NM_005422
11 120998460 120999053 TECTA NM_005422
11 121000346 121000920 TECTA NM_005422
11 121008129 121008731 TECTA NM_005422
11 121016263 121016825 TECTA NM_005422
11 121023589 121023789 TECTA NM_005422
11 121028549 121028933 TECTA NM_005422
11 121030843 121031130 TECTA NM_005422
11 121032783 121033079 TECTA NM_005422
11 121035981 121036092 TECTA NM_005422
11 121037286 121037489 TECTA NM_005422
11 121038762 121038926 TECTA NM_005422
11 121039385 121039634 TECTA NM_005422
11 121058540 121058703 TECTA NM_005422
11 121059788 121059876 TECTA NM_005422
11 121060472 121060589 TECTA NM_005422
11 121061414 121061515 TECTA NM_005422
19 10218326 10218411 SNORD105 NR_004381
17 62223437 62223517 SNORD104 NR_004380
X 109468216 109468288 SNORD96B NR_004379
2 86362992 86363129 SNORD94 NR_004378
1 231762560 231762680 DISC1 NM_001164555
1 231829571 231830551 DISC1 NM_001164555
1 231885671 231886365 DISC1 NM_001164555
16 5094122 5094479 C16orf89 NM_001098514
16 5097878 5097965 C16orf89 NM_001098514
16 5105246 5105351 C16orf89 NM_001098514
16 5106053 5106189 C16orf89 NM_001098514
16 5108493 5108611 C16orf89 NM_001098514
16 5110286 5110437 C16orf89 NM_001098514
16 5112425 5112575 C16orf89 NM_001098514
16 5115701 5116146 C16orf89 NM_001098514

If you need other information or more data, please don't hesitate to contact me.

Bests,

Koen

[slzhao]

Hello Koen,

I checked your results and found that: the "genesPassQC.bed" file was right
but the "genesPassQCwithGC.bed" was not correct. So the problem should be
in GC content calculation.
And I think the problem is the different chromosome formats in gtf and
fasta file. Your gtf files may have chromosome format like "chr1", while
your fasta file have chromosome format like "1". That's the problem.

I've updated ExonDel to version 1.01 which can handle different
formats of chromosome.
Would you please try that version and I think it will work.

Please let me know if you have any other questions. Thank you!

Best,
Shilin

2015-04-07 4:06 GMT-05:00 Koen Hendriks notifications@github.com:

Hello Shilin,

I've run ExonDel again and this is in my covered_percentage file:

#bin name om strand txStart txEnd cdsStart cdsEnd exonCount exonStarts
exonEnds score name2 cdsStartStat cdsEndStat exonFrames coveredBP
coveredExon
19 NM_001291929 11 - 89057521 89223909 89059923 89223852 17
89057521,89069012,89070614,89073230,89075241,89088129,89106599,89133184,89133382,89135493,89155069,89165951,89173855,89177302,89182607,89184952,89223774,
89060044,89069113,89070683,89073339,89075361,89088211,89106660,89133247,89133547,89135710,89155150,89166024,89173883,89177400,89182692,89185063,89223909,
0 NOX4 cmpl cmpl 2,0,0,2,2,1,0,0,0,2,2,1,0,1,0,0,0, 0.400434992750121
0.882352941176471
985 NM_016039 14 + 52456227 52471420 52456357 52471234 8
52456227,52458034,52460440,52465211,52466425,52468515,52470911,52471079,
52456418,52458159,52460540,52465298,52466514,52468584,52470960,52471420, 0
C14orf166 cmpl cmpl 0,1,0,1,1,0,0,1, 0.768649669499528 1
858 NM_006739 22 + 35796115 35820495 35796431 35820248 17
35796115,35796423,35799199,35799406,35802545,35804400,35806736,35808502,35809867,35811821,35812331,35812630,35813736,35815876,35817310,35819206,35820146,
35796201,35796598,35799326,35799535,35802718,35804556,35806903,35808674,35809979,35811965,35812397,35812807,35813849,35816005,35817453,35819334,35820495,
0 MCM5 cmpl cmpl -1,0,2,0,0,2,2,1,2,0,0,0,0,2,2,1,0, 0.873195474053843
0.941176470588235
1761 NM_032385 5 - 154198051 154230213 154199875 154217738 9
154198051,154200819,154202031,154202946,154210360,154214184,154214402,154217690,154230042,
154200032,154200986,154202137,154203152,154210482,154214288,154214494,154217738,154230213,
0 FAXDC2 cmpl cmpl 2,0,2,0,1,2,0,0,-1, 0.349634065202928 0.888888888888889
587 NM_021034 11 - 319672 320914 319837 320813 2 319672,320564,
319990,320914, 0 IFITM3 cmpl cmpl 0,0, 0.749253731343284 1
1162 NM_020932 X + 75648045 75651746 75648323 75651197 1 75648045,
75651746, 0 MAGEE1 cmpl cmpl 0, 0.809832522960562 1
13 NM_020929 11 - 40135750 41481186 40135919 40137842 5
40135750,40162350,40341177,40669691,41480980,
40137884,40162403,40341271,40669828,41481186, 0 LRRC4C cmpl cmpl
0,-1,-1,-1,-1, 0.769874476987448 0.2
1352 NM_021029 X + 100645877 100651142 100645923 100650736 5
100645877,100646446,100646742,100650322,100650715,
100646034,100646552,100646810,100650445,100651142, 0 RPL36A cmpl cmpl
0,0,1,0,0, 0.488713318284424 1
1688 NM_032378 8 - 144661866 144679845 144661961 144672251 10
144661866,144662181,144662675,144663223,144663398,144668388,144668898,144671160,144672777,144679517,
144662000,144662376,144662897,144663324,144663498,144668460,144669022,144672251,144672908,144679845,
0 EEF1D cmpl cmpl 0,0,0,1,0,0,2,0,-1,-1, 0.80622009569378 0.8
106 NR_002833 7 - 35120898 35225774 35225774 35225774 22

genesPassQC.bed contains the following±

14 52456227 52456418 C14orf166 NM_016039
14 52458034 52458159 C14orf166 NM_016039
14 52460440 52460540 C14orf166 NM_016039
14 52465211 52465298 C14orf166 NM_016039
14 52466425 52466514 C14orf166 NM_016039
14 52468515 52468584 C14orf166 NM_016039
14 52470911 52470960 C14orf166 NM_016039
14 52471079 52471420 C14orf166 NM_016039
11 319672 319990 IFITM3 NM_021034
11 320564 320914 IFITM3 NM_021034
X 75648045 75651746 MAGEE1 NM_020932
X 100645877 100646034 RPL36A NM_021029
X 100646446 100646552 RPL36A NM_021029
X 100646742 100646810 RPL36A NM_021029
X 100650322 100650445 RPL36A NM_021029
X 100650715 100651142 RPL36A NM_021029
19 48373722 48374824 SULT2A1 NM_003167
19 48377913 48378091 SULT2A1 NM_003167
19 48382292 48382387 SULT2A1 NM_003167
19 48385340 48385467 SULT2A1 NM_003167
19 48386833 48387042 SULT2A1 NM_003167
19 48389378 48389654 SULT2A1 NM_003167
1 26856248 26856474 RPS6KA1 NM_002953
1 26863415 26863460 RPS6KA1 NM_002953
1 26873357 26873474 RPS6KA1 NM_002953
1 26873679 26873761 RPS6KA1 NM_002953
1 26877887 26877968 RPS6KA1 NM_002953
1 26878134 26878214 RPS6KA1 NM_002953
1 26879881 26879988 RPS6KA1 NM_002953
1 26880704 26880742 RPS6KA1 NM_002953
1 26881086 26881229 RPS6KA1 NM_002953
1 26881641 26881712 RPS6KA1 NM_002953
1 26882027 26882116 RPS6KA1 NM_002953
1 26883144 26883209 RPS6KA1 NM_002953
1 26883488 26883591 RPS6KA1 NM_002953
1 26885297 26885428 RPS6KA1 NM_002953
1 26887216 26887342 RPS6KA1 NM_002953
1 26887535 26887625 RPS6KA1 NM_002953
1 26887995 26888154 RPS6KA1 NM_002953
1 26897939 26898101 RPS6KA1 NM_002953
1 26898339 26898416 RPS6KA1 NM_002953
1 26898666 26898784 RPS6KA1 NM_002953
1 26899714 26899852 RPS6KA1 NM_002953
1 26900569 26901520 RPS6KA1 NM_002953
20 36932551 36932755 BPI NM_001725
20 36935968 36936083 BPI NM_001725
20 36937331 36937460 BPI NM_001725
20 36938892 36939054 BPI NM_001725
20 36940275 36940339 BPI NM_001725
20 36946814 36946878 BPI NM_001725
20 36948584 36948676 BPI NM_001725
20 36952271 36952448 BPI NM_001725
20 36953175 36953235 BPI NM_001725
20 36954666 36954834 BPI NM_001725
20 36955989 36956057 BPI NM_001725
20 36959449 36959492 BPI NM_001725
20 36962831 36962895 BPI NM_001725
20 36963999 36964076 BPI NM_001725
20 36965547 36965905 BPI NM_001725
16 11361713 11361869 TNP2 NM_005425
16 11362719 11363160 TNP2 NM_005425
11 120973374 120973438 TECTA NM_005422
11 120976539 120976673 TECTA NM_005422
11 120979919 120980207 TECTA NM_005422
11 120983780 120983918 TECTA NM_005422
11 120984261 120984427 TECTA NM_005422
11 120989014 120989427 TECTA NM_005422
11 120996010 120996581 TECTA NM_005422
11 120998460 120999053 TECTA NM_005422
11 121000346 121000920 TECTA NM_005422
11 121008129 121008731 TECTA NM_005422
11 121016263 121016825 TECTA NM_005422
11 121023589 121023789 TECTA NM_005422
11 121028549 121028933 TECTA NM_005422
11 121030843 121031130 TECTA NM_005422
11 121032783 121033079 TECTA NM_005422
11 121035981 121036092 TECTA NM_005422
11 121037286 121037489 TECTA NM_005422
11 121038762 121038926 TECTA NM_005422
11 121039385 121039634 TECTA NM_005422
11 121058540 121058703 TECTA NM_005422
11 121059788 121059876 TECTA NM_005422
11 121060472 121060589 TECTA NM_005422
11 121061414 121061515 TECTA NM_005422
19 10218326 10218411 SNORD105 NR_004381
17 62223437 62223517 SNORD104 NR_004380
X 109468216 109468288 SNORD96B NR_004379
2 86362992 86363129 SNORD94 NR_004378
1 231762560 231762680 DISC1 NM_001164555
1 231829571 231830551 DISC1 NM_001164555
1 231885671 231886365 DISC1 NM_001164555
16 5094122 5094479 C16orf89 NM_001098514
16 5097878 5097965 C16orf89 NM_001098514
16 5105246 5105351 C16orf89 NM_001098514
16 5106053 5106189 C16orf89 NM_001098514
16 5108493 5108611 C16orf89 NM_001098514
16 5110286 5110437 C16orf89 NM_001098514
16 5112425 5112575 C16orf89 NM_001098514
16 5115701 5116146 C16orf89 NM_001098514

If you need other information or more data, please don't hesitate to
contact me.

Bests,

Koen

—
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#2 (comment).

[pineapple216]

Hi Shilin,

Today I've tried running ExonDel v1.04.
It unfortunately still gives an error.

The ExonDel.rLog file contains the following:

Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: read.bigFile -> read.delim -> read.table
Execution halted

Hopefully you can shed some light on this.

Bests,

Koen

[slzhao]

Hello Koen,

I think we can fix the "Error in read.table ~~" problem with the following
steps:

1. Would you please check the content in genesPassQCwithGC.bed.depth and
   genesPassWCwithGC.bed. Is it empty or has some content? Would you please
   send the content to me?
2. If the .depth file is empty, then there are some issues in counting
   reads from bam file. It may related to format in bed/gtf/fa file. We can
   discuss it later;
3. If the .depth file is not empty, then it should be some bugs in R code.
   Is there any other information in rlog file? I think there should be a
   "loading some file to R" message so that I can know which file is wrong.
   And please also send me the genesPassQCwithGC.bed.depth and
   genesPassWCwithGC.bed file. So that I can try to read them in my computer.

Thank you!

Best,
Shilin

2015-05-28 5:53 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

Today I've tried running ExonDel v1.04.
It unfortunately still gives an error.

The ExonDel.rLog file contains the following:

Error in read.table(file = file, header = header, sep = sep, quote =
quote, :
no lines available in input
Calls: read.bigFile -> read.delim -> read.table
Execution halted

Hopefully you can shed some light on this.

Bests,

Koen

—
Reply to this email directly or view it on GitHub
#2 (comment).

[pineapple216]

Hi Shilin,

Here's some info to help you solve it.

1. genesPassQCwithGC.bed.depth contains:

DNA03-03099-BRCA1_test
DNA04-04960-BRCA1
DNA05-02178-BRCA1
DNA05-02206-BRCA1
DNA07-07992-BRCA1
DNA07-09019-BRCA1_test
`
which is a list of my samples.

genesPassWCwithGC.bed is empty.

The problem might be in my gtf file.

Bests,

Koen

[slzhao]

Hi Koen,

Yes. I think it is related to the format of gtf file. Would you please
compare your gft file with the description in README:

The .gtf and .bed files could be downloaded at UCSC table browser
http://genome.ucsc.edu/cgi-bin/hgTables?command=start. To download a gtf
file with correct format, please select track as RefSeq Genes in UCSC table
browser. The format of these files were:

#gtf file:
#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount
exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames

I've also updated ExonDel to 1.05 to add a warning message if gtf file with
incorrect format is used.
Please let me know if you have any other questions.

Best,
Shilin

2015-05-29 7:12 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

Here's some info to help you solve it.

1. genesPassQCwithGC.bed.depth contains:

DNA03-03099-BRCA1_test
DNA04-04960-BRCA1
DNA05-02178-BRCA1
DNA05-02206-BRCA1
DNA07-07992-BRCA1
DNA07-09019-BRCA1_test
`
which is a list of my samples.

genesPassWCwithGC.bed is empty.

The problem might be in my gtf file.

Bests,

Koen

—
Reply to this email directly or view it on GitHub
#2 (comment).

[pineapple216]

Hi Shilin,

Thanks for the quick reply.

I've run v1.05 and checked the gtf file and it seems mine is correct.
ExonDel doesn't display a warning about my gtf file format.

Unfortunately, the read.table error still persists.

Koen

[slzhao]

Hi Koen,

So the "genesPassQCwithGC.bed" file is still empty? What about the
"genesPassQC.bed" file?
If both of them are empty. There is a "Finish BED file (cover SomeNumber
base pairs)" message in log file. What is the SomeNumber in it? It should
be larger than 0.

Best,
Shilin

2015-06-03 6:28 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

Thanks for the quick reply.

I've run v1.05 and checked the gtf file and it seems mine is correct.
ExonDel doesn't display a warning about my gtf file format.

Unfortunately, the read.table error still persists.

Koen

—
Reply to this email directly or view it on GitHub
#2 (comment).

[pineapple216]

Hi Shilin,

Yes, the "genesPassQCwithGC.bed" file is still empty, as is the "genesPassQC.bed" file.
The log file is empty, the screen output when I run the tool, starts with this:

[Tue Jun 9 10:15:03 2015] All genes will be used
[Tue Jun 9 10:15:03 2015] Loading BED file
[Tue Jun 9 10:15:03 2015] Finish BED file (cover 8119 base pairs)
[Tue Jun 9 10:15:03 2015] Loading RefSeq file
[Tue Jun 9 10:15:06 2015] Finish RefSeq file
[Tue Jun 9 10:15:06 2015] Loading fasta file and caculating GC content
[Tue Jun 9 10:15:33 2015] Finish fasta file
[Tue Jun 9 10:15:33 2015] Loading genesPassQCwithGC.bed
[Tue Jun 9 10:15:33 2015] Processing bam files

Best regards,

Koen

[slzhao]

Thanks Koen.
Then what about the "covered_percentage" file, is it empty?
I think it should be a file format issue. Would you please send me some
lines from your bed file and gtf file? So that I can try to test it.
Thank you.

Best,
Shilin

2015-06-09 3:44 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

Yes, the "genesPassQCwithGC.bed" file is still empty, as is the
"genesPassQC.bed" file.
The log file is empty, the screen output when I run the tool, starts with
this:

[Tue Jun 9 10:15:03 2015] All genes will be used
[Tue Jun 9 10:15:03 2015] Loading BED file
[Tue Jun 9 10:15:03 2015] Finish BED file (cover 8119 base pairs)
[Tue Jun 9 10:15:03 2015] Loading RefSeq file
[Tue Jun 9 10:15:06 2015] Finish RefSeq file
[Tue Jun 9 10:15:06 2015] Loading fasta file and caculating GC content
[Tue Jun 9 10:15:33 2015] Finish fasta file
[Tue Jun 9 10:15:33 2015] Loading genesPassQCwithGC.bed
[Tue Jun 9 10:15:33 2015] Processing bam files

Best regards,

Koen

—
Reply to this email directly or view it on GitHub
#2 (comment).

[pineapple216]

Hi Shilin,

No, the covered percentage file contains the following±

#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames c
overedBP coveredExon
1059 NR_004380 chr17 + 62223437 62223517 62223517 62223517 1 62223437, 62223517, 0 SNORD104 unk unk -
1, 0 0
637 NR_040089 chr17 - 6888441 6915653 6915653 6915653 3 6888441,6913114,6915514, 6888859,6913208,6915653, 0 ALOX12-AS1 unk unk -
1,-1,-1, 0 0
16 NR_036146 chr17 + 60798857 61268734 61268734 61268734 4 60798857,60798903,60887536,61268699, 60798873,60798908,60887552,612687
34, 0 MIR548W unk unk -1,-1,-1,-1, 0 0
958 NR_038458 chr17 + 48944039 48945732 48945732 48945732 2 48944039,48944856, 48944578,48945732, 0 TOB1-AS1 u
nk unk -1,-1, 0 0
1150 NM_001145298 chr17 - 74077073 74099868 74079728 74099773 19 74077073,74080086,74080328,74080597,74081394,74081757,74082160,74083734,7
4084140,74084544,74084851,74085255,74086409,74090494,74093876,74097351,74097759,74099441,74099713, 74079831,74080220,74080370,74080661,74081490,74081878,74082226,74083801,74084203,
74084643,74085004,74085401,74086478,74090662,74094099,74097457,74097944,74099507,74099868, 0 EXOC7 cmpl cmpl 2,0,0,2,2,1,1,0,0,0,0,1,1,1,0,2,0,0,0, 0 0
597 NM_000934 chr17 + 1646129 1658559 1648289 1657828 10 1646129,1648285,1648468,1648626,1649001,1650312,1650602,1651891,1655879,1657415, 1646202,1648352,1
648507,1648689,1649203,1650456,1650806,1652034,1656084,1658559, 0 SERPINF2 cmpl cmpl -1,0,0,0,0,1,1,1,0,1, 0 0
114 NM_004382 chr17 + 43861645 43913194 43861910 43912130 13 43861645,43884375,43893828,43898720,43906580,43907459,43907782,43908245,4
3910503,43910817,43911079,43911372,43911989, 43861943,43884463,43893948,43898806,43906687,43907580,43907936,43908306,43910576,43910903,43911215,43911414,43913194, 0 CRHR1 c
mpl cmpl 0,0,1,1,0,2,0,1,2,0,2,0,0, 0 0
1181 NM_000199 chr17 - 78183078 78194199 78184250 78194112 8 78183078,78185869,78187602,78187970,78188413,78188831,78190830,78194024,78184810,78186073,78187684,78188127,78188564,78188937,78190991,78194199, 0 SGSH cmpl cmpl 1,1,0,2,1,0,1,0, 0 0
724 NM_001145127 chr17 + 18281078 18292960 18284251 18291562 11 18281078,18284215,18284680,18284916,18285826,18286139,18286338,18286584,1
8286805,18291532,18292170, 18281297,18284314,18284835,18285044,18285952,18286178,18286499,18286692,18286901,18291602,18292960, 0 EVPLL cmpl cmpl -1,0,0,2,1,1,1,0,
0,0,-1, 0 0
12 NM_001094 chr17 - 31340105 32483825 31340982 32483551 10 31340105,31342988,31344622,31348236,31350878,31352943,31355259,31415880,3
1438934,32482996, 31341084,31343057,31344702,31348328,31351032,31353000,31355410,31416008,31439085,32483825, 0 ASIC2 cmpl cmpl 0,0,1,2,1,1,0,1,0,0, 0 0
784 NM_000625 chr17 - 26083791 26127555 26084271 26125835 27 26083791,26085906,26087055,26087648,26088169,26089823,26091006,26092560,2
6093535,26094730,26096002,26096560,26097938,26099333,26100186,26101282,26105715,26105907,26107792,26108061,26109040,26109969,26114703,26115834,26116629,26125725,26127364, 26084379,
26086101,26087204,26087770,26088257,26090031,26091170,26092742,26093614,26094863,26096177,26096610,26098043,26099478,26100269,26101477,26105817,26106082,26107932,26108203,26109132,26110
132,26114852,26115957,26116714,26125908,26127555, 0 NOS2 cmpl cmpl 0,0,1,2,1,0,1,2,1,0,2,0,0,2,0,0,0,2,0,2,0,2,0,0,2,0,-1, 0 0
880 NM_001838 chr17 - 38710021 38721736 38710993 38721661 3 38710021,38715144,38721651, 38712070,38715194,38721736, 0 C
CR7 cmpl cmpl 0,1,0, 0 0
13 NM_001991 chr17 - 40852292 40897071 40854549 40880959 21 40852292,40854894,40855757,40856619,40857105,40858024,40859975,40860893,4
0861863,40864306,40865226,40869993,40870471,40871122,40872290,40874812,40876322,40879652,40880842,40882845,40897028, 40854610,40854979,40855838,40856701,40857201,40858203,40860101,40
860934,40861955,40864503,40865407,40870085,40870635,40871225,40872467,40874933,40876442,40879781,40880970,40882936,40897071, 0 EZH1 cmpl cmpl 2,1,1,0,0,1,1,2,0,1,0,1,2
,1,1,0,0,0,0,-1,-1, 0 0

My bed file looks like this:

chr17 41197659 41197893 BRCA1_Ex23
chr17 41199626 41199751 BRCA1_Ex22
chr17 41201100 41201260 BRCA1_Ex21
chr17 41203038 41203163 BRCA1_Ex20
chr17 41209032 41209237 BRCA1_Ex19
chr17 41215295 41215436 BRCA1_Ex18
chr17 41215857 41216035 BRCA1_Ex17

And my GTF file starts with this:

#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames
19 NM_001291929 chr11 - 89057521 89223909 89059923 89223852 17 89057521,89069012,89070614,89073230,89075241,89088129,89106599,89133184,89133382,89135493,89155069,89165951,89173855,89177302,89182607,89184952,89223774, 89060044,89069113,89070683,89073339,89075361,89088211,89106660,89133247,89133547,89135710,89155150,89166024,89173883,89177400,89182692,89185063,89223909, 0 NOX4 cmpl cmpl 2,0,0,2,2,1,0,0,0,2,2,1,0,1,0,0,0,
985 NM_016039 chr14 + 52456227 52471420 52456357 52471234 8 52456227,52458034,52460440,52465211,52466425,52468515,52470911,52471079,52456418,52458159,52460540,52465298,52466514,52468584,52470960,52471420, 0 C14orf166 cmpl cmpl 0,1,0,1,1,0,0,1,
858 NM_006739 chr22 + 35796115 35820495 35796431 35820248 17 35796115,35796423,35799199,35799406,35802545,35804400,35806736,35808502,35809867,35811821,35812331,35812630,35813736,35815876,35817310,35819206,35820146, 35796201,35796598,35799326,35799535,35802718,35804556,35806903,35808674,35809979,35811965,35812397,35812807,35813849,35816005,35817453,35819334,35820495, 0 MCM5 cmpl cmpl -1,0,2,0,0,2,2,1,2,0,0,0,0,2,2,1,0,
1761 NM_032385 chr5 - 154198051 154230213 154199875 154217738 9 154198051,154200819,154202031,154202946,154210360,154214184,154214402,154217690,154230042, 154200032,154200986,154202137,154203152,154210482,154214288,154214494,154217738,154230213, 0 FAXDC2 cmpl cmpl 2,0,2,0,1,2,0,0,-1,
587 NM_021034 chr11 - 319672 320914 319837 320813 2 319672,320564, 319990,320914, 0 IFITM3 cmpl cmpl 0,0,
1162 NM_020932 chrX + 75648045 75651746 75648323 75651197 1 75648045, 75651746, 0 MAGEE1 cmpl cmpl 0,
13 NM_020929 chr11 - 40135750 41481186 40135919 40137842 5 40135750,40162350,40341177,40669691,41480980, 40137884,40162403,40341271,40669828,41481186, 0 LRRC4C cmpl cmpl 0,-1,-1,-1,-1,
1352 NM_021029 chrX + 100645877 100651142 100645923 100650736 5 100645877,100646446,100646742,100650322,100650715, 100646034,100646552,100646810,100650445,100651142, 0 RPL36A cmpl cmpl 0,0,1,0,0,
1688 NM_032378 chr8 - 144661866 144679845 144661961 144672251 10 144661866,144662181,144662675,144663223,144663398,144668388,144668898,144671160,144672777,144679517, 144662000,144662376,144662897,144663324,144663498,144668460,144669022,144672251,144672908,144679845, 0 EEF1D cmpl cmpl 0,0,0,1,0,0,2,0,-1,-1,

Best,

Koen

.

[slzhao]

Hello Koen,

I think here is the issue:
There are two settings in the ExonDel config file:
#Minimal percent of covered base pairs for each exon
exon_bp_cover_threshold=0.1
#Minimal percent of covered exons for each gene
overall_exon_count_threshold=1

Here overall_exon_count_threshold=1 means only when all exons for one gene
(defined in gtf file) is covered in bed file, it will be used for Exon
deletion detection. So that we can make sure the exons with 0 reads are due
to "deletion", not due to "not captured in experiment". And with this
restriction we can decrease the false discover rate.
You can set it to a lower value, for example, overall_exon_count_threshold=0.5
and I think it should work.

I will update it in a newer version.Thank you!

Best,
Shilin

2015-06-10 6:07 GMT-05:00 Koen Hendriks notifications@github.com:

Hi Shilin,

No, the covered percentage file contains the following±

#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts
exonEnds score name2 cdsStartStat cdsEndStat exonFrames c
overedBP coveredExon
1059 NR_004380 chr17 + 62223437 62223517 62223517 62223517 1 62223437,
62223517, 0 SNORD104 unk unk -
1, 0 0
637 NR_040089 chr17 - 6888441 6915653 6915653 6915653 3
6888441,6913114,6915514, 6888859,6913208,6915653, 0 ALOX12-AS1 unk unk -
1,-1,-1, 0 0
16 NR_036146 chr17 + 60798857 61268734 61268734 61268734 4
60798857,60798903,60887536,61268699, 60798873,60798908,60887552,612687
34, 0 MIR548W unk unk -1,-1,-1,-1, 0 0
958 NR_038458 chr17 + 48944039 48945732 48945732 48945732 2
48944039,48944856, 48944578,48945732, 0 TOB1-AS1 u
nk unk -1,-1, 0 0
1150 NM_001145298 chr17 - 74077073 74099868 74079728 74099773 19
74077073,74080086,74080328,74080597,74081394,74081757,74082160,74083734,7
4084140,74084544,74084851,74085255,74086409,74090494,74093876,74097351,74097759,74099441,74099713,
74079831,74080220,74080370,74080661,74081490,74081878,74082226,74083801,74084203,
74084643,74085004,74085401,74086478,74090662,74094099,74097457,74097944,74099507,74099868,
0 EXOC7 cmpl cmpl 2,0,0,2,2,1,1,0,0,0,0,1,1,1,0,2,0,0,0, 0 0
597 NM_000934 chr17 + 1646129 1658559 1648289 1657828 10
1646129,1648285,1648468,1648626,1649001,1650312,1650602,1651891,1655879,1657415,
1646202,1648352,1
648507,1648689,1649203,1650456,1650806,1652034,1656084,1658559, 0 SERPINF2
cmpl cmpl -1,0,0,0,0,1,1,1,0,1, 0 0
114 NM_004382 chr17 + 43861645 43913194 43861910 43912130 13
43861645,43884375,43893828,43898720,43906580,43907459,43907782,43908245,4
3910503,43910817,43911079,43911372,43911989,
43861943,43884463,43893948,43898806,43906687,43907580,43907936,43908306,43910576,43910903,43911215,43911414,43913194,
0 CRHR1 c
mpl cmpl 0,0,1,1,0,2,0,1,2,0,2,0,0, 0 0
1181 NM_000199 chr17 - 78183078 78194199 78184250 78194112 8
78183078,78185869,78187602,78187970,78188413,78188831,78190830,78194024,78184810,78186073,78187684,78188127,78188564,78188937,78190991,78194199,
0 SGSH cmpl cmpl 1,1,0,2,1,0,1,0, 0 0
724 NM_001145127 chr17 + 18281078 18292960 18284251 18291562 11
18281078,18284215,18284680,18284916,18285826,18286139,18286338,18286584,1
8286805,18291532,18292170,
18281297,18284314,18284835,18285044,18285952,18286178,18286499,18286692,18286901,18291602,18292960,
0 EVPLL cmpl cmpl -1,0,0,2,1,1,1,0,
0,0,-1, 0 0
12 NM_001094 chr17 - 31340105 32483825 31340982 32483551 10
31340105,31342988,31344622,31348236,31350878,31352943,31355259,31415880,3
1438934,32482996,
31341084,31343057,31344702,31348328,31351032,31353000,31355410,31416008,31439085,32483825,
0 ASIC2 cmpl cmpl 0,0,1,2,1,1,0,1,0,0, 0 0
784 NM_000625 chr17 - 26083791 26127555 26084271 26125835 27
26083791,26085906,26087055,26087648,26088169,26089823,26091006,26092560,2
6093535,26094730,26096002,26096560,26097938,26099333,26100186,26101282,26105715,26105907,26107792,26108061,26109040,26109969,26114703,26115834,26116629,26125725,26127364,
26084379,

26086101,26087204,26087770,26088257,26090031,26091170,26092742,26093614,26094863,26096177,26096610,26098043,26099478,26100269,26101477,26105817,26106082,26107932,26108203,26109132,26110
132,26114852,26115957,26116714,26125908,26127555, 0 NOS2 cmpl cmpl
0,0,1,2,1,0,1,2,1,0,2,0,0,2,0,0,0,2,0,2,0,2,0,0,2,0,-1, 0 0
880 NM_001838 chr17 - 38710021 38721736 38710993 38721661 3
38710021,38715144,38721651, 38712070,38715194,38721736, 0 C
CR7 cmpl cmpl 0,1,0, 0 0
13 NM_001991 chr17 - 40852292 40897071 40854549 40880959 21
40852292,40854894,40855757,40856619,40857105,40858024,40859975,40860893,4
0861863,40864306,40865226,40869993,40870471,40871122,40872290,40874812,40876322,40879652,40880842,40882845,40897028,
40854610,40854979,40855838,40856701,40857201,40858203,40860101,40
860934,40861955,40864503,40865407,40870085,40870635,40871225,40872467,40874933,40876442,40879781,40880970,40882936,40897071,
0 EZH1 cmpl cmpl 2,1,1,0,0,1,1,2,0,1,0,1,2
,1,1,0,0,0,0,-1,-1, 0 0

My bed file looks like this:

chr17 41197659 41197893 BRCA1_Ex23
chr17 41199626 41199751 BRCA1_Ex22
chr17 41201100 41201260 BRCA1_Ex21
chr17 41203038 41203163 BRCA1_Ex20
chr17 41209032 41209237 BRCA1_Ex19
chr17 41215295 41215436 BRCA1_Ex18
chr17 41215857 41216035 BRCA1_Ex17

And my GTF file starts with this:

#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts
exonEnds score name2 cdsStartStat cdsEndStat exonFrames
19 NM_001291929 chr11 - 89057521 89223909 89059923 89223852 17
89057521,89069012,89070614,89073230,89075241,89088129,89106599,89133184,89133382,89135493,89155069,89165951,89173855,89177302,89182607,89184952,89223774,
89060044,89069113,89070683,89073339,89075361,89088211,89106660,89133247,89133547,89135710,89155150,89166024,89173883,89177400,89182692,89185063,89223909,
0 NOX4 cmpl cmpl 2,0,0,2,2,1,0,0,0,2,2,1,0,1,0,0,0,
985 NM_016039 chr14 + 52456227 52471420 52456357 52471234 8
52456227,52458034,52460440,52465211,52466425,52468515,52470911,52471079,52456418,52458159,52460540,52465298,52466514,52468584,52470960,52471420,
0 C14orf166 cmpl cmpl 0,1,0,1,1,0,0,1,
858 NM_006739 chr22 + 35796115 35820495 35796431 35820248 17
35796115,35796423,35799199,35799406,35802545,35804400,35806736,35808502,35809867,35811821,35812331,35812630,35813736,35815876,35817310,35819206,35820146,
35796201,35796598,35799326,35799535,35802718,35804556,35806903,35808674,35809979,35811965,35812397,35812807,35813849,35816005,35817453,35819334,35820495,
0 MCM5 cmpl cmpl -1,0,2,0,0,2,2,1,2,0,0,0,0,2,2,1,0,
1761 NM_032385 chr5 - 154198051 154230213 154199875 154217738 9
154198051,154200819,154202031,154202946,154210360,154214184,154214402,154217690,154230042,
154200032,154200986,154202137,154203152,154210482,154214288,154214494,154217738,154230213,
0 FAXDC2 cmpl cmpl 2,0,2,0,1,2,0,0,-1,
587 NM_021034 chr11 - 319672 320914 319837 320813 2 319672,320564,
319990,320914, 0 IFITM3 cmpl cmpl 0,0,
1162 NM_020932 chrX + 75648045 75651746 75648323 75651197 1 75648045,
75651746, 0 MAGEE1 cmpl cmpl 0,
13 NM_020929 chr11 - 40135750 41481186 40135919 40137842 5
40135750,40162350,40341177,40669691,41480980,
40137884,40162403,40341271,40669828,41481186, 0 LRRC4C cmpl cmpl
0,-1,-1,-1,-1,
1352 NM_021029 chrX + 100645877 100651142 100645923 100650736 5
100645877,100646446,100646742,100650322,100650715,
100646034,100646552,100646810,100650445,100651142, 0 RPL36A cmpl cmpl
0,0,1,0,0,
1688 NM_032378 chr8 - 144661866 144679845 144661961 144672251 10
144661866,144662181,144662675,144663223,144663398,144668388,144668898,144671160,144672777,144679517,
144662000,144662376,144662897,144663324,144663498,144668460,144669022,144672251,144672908,144679845,
0 EEF1D cmpl cmpl 0,0,0,1,0,0,2,0,-1,-1,

Best,

Koen

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