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remove reptitive regions on paired-end #58

Merged
merged 113 commits into from
Mar 6, 2015
Merged

remove reptitive regions on paired-end #58

merged 113 commits into from
Mar 6, 2015

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olgabot
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@olgabot olgabot commented Jan 31, 2015

to fix this: #57

should remove repetitive regions on paired-end too, so that the paired end and single end are comparable

@olgabot olgabot force-pushed the remove_repetitive_regions_paired_end branch from eae7f7f to c9fe86b Compare February 10, 2015 04:47
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olgabot commented Feb 12, 2015

ready to merge

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olgabot commented Feb 21, 2015

doesn't work on single-end reads.... I'm an idiot and in my testing copied my PE manifest file to the SE name. stay tuned.

@gpratt
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gpratt commented Feb 21, 2015

Try to do a rebase / pull I updated repetitive elements removal to use
star, might make your job a bit easier/ it will need to be integrated
anyway.
On Feb 21, 2015 11:17 AM, "Olga Botvinnik" notifications@github.com wrote:

doesn't work on single-end reads.... I'm an idiot and in my testing copied
my PE manifest file to the SE name. stay tuned.

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

@olgabot
Add a #!/usr/bin/env python line at the top to specifically call python
5dc1595
@olgabot
remove reptitive regions on paired-end
f0b2ea7
@olgabot
Add trimgalore
6d322de
@olgabot
start writing out removing replicates and mapping to repetitive regio…
89ae2f9 
…ns for paired end reads
@olgabot
MapRepetitiveRegions --> MapRepetitiveRegions2
a10de10
@olgabot
I have no idea how to continue strings on multiple lines in scala
e4bfd62
@olgabot
return tuple in scala
9bcf485
@olgabot
fix variable names
ea94b9f
@olgabot
fix up typos and variable names
bbed512
@olgabot
fix up trimgalore calls
6d23c23
@olgabot
tuples are hard
5f5cddf
@olgabot
add declaration of filteredFastqPair
12271c0
@olgabot
scala doesn't allow assignment to tuples of exisiting variables: http…
84c814a 
…://stackoverflow.com/questions/3348751/scala-multiple-assignment-to-existing-variable
@olgabot
fix declaration
419fd44
@olgabot
do tuple gymnastics so scala is happy
ad4a1c5
@olgabot
fix up calls to trimGalore
2d58d40
@olgabot
still fixing trimgalore
d676a35
@olgabot
fix up call to trimgalore
9b2a80e
@olgabot
missing comma
d37d7f8
@olgabot
remove adapter from trimgalore call and hope that it references the o…
c53a7fe 
…uter scope
@olgabot
Change this.adapter to this.adapterList in trimGalroe
7aa37ae
@olgabot
move system exit if strict but not trimgalore
8a06a57
@olgabot
add dependency of maprepetitiveregions to trimgalore
57a15ff
@olgabot
add other arguments to maprepetitiveregions
4c47921
@olgabot
fix up arguments for maprepetitiveregions
714fb12
@olgabot
remove fastqpair from single end stringent jobs
90c7d76
olgabot and others added 25 commits March 6, 2015 10:18
@olgabot
trying to fix paired/nonpaired logic for TrimGalore and MapRepetitive…
82a3d72 
…Regions2
@olgabot
Fix logic of this.outNoRepetitive for mapRepetitiveRegions
4da80fa
@olgabot
trying to fix some weird cycle introduced intro graph
74f7810
@olgabot
Make arguments into mapRepetitiveRegions explicit to avoid cycles
b1eb217
@olgabot
remove originalFastqFile as argument
dde40bc
@olgabot
fix output filename of trim_galore
3ddc8ab
@olgabot
Change trim_galore output to the correct *_val_{1,2}.fq instead of *_…
12b6b8b 
…trimmed.fq
@olgabot
updated STAR path
5c66b68
@olgabot
quantify read counts on repetitive regions
6475ed4
@olgabot
Don't rename files that don't exist
3e0c04a
@olgabot
add definition of countRepetitiveRegions
e3a79b5
@olgabot
fix up call to countRepetitiveRegions
6de932c
@olgabot
comment out RNA editing makefile and count_tags for testing
555e987
@olgabot
change name of repetitive aligned data to not overlap with the non re…
f083eda 
…petitive aligned one
@olgabot
debugging single end
f21e1a5
@olgabot
fix logic
c63690f
@olgabot
var --> val
d0fea74
@olgabot
change the way trimmedFastqPair is specified
be1fcbc
@olgabot
change logic of stringentJobsTrimGalore to deal with single end better
f0cef22
@olgabot
filteredFastq as null
4d61825
@olgabot
make fake fastq pair for single end
23f0ff8
@olgabot
fix naming
eda1a11
@olgabot
switch logic from checking null to relying on paired Boolean
838329b
@olgabot
move filteredFastPair out of if/else
87f57ad
@olgabot
try to change order fake fastq pair
912eda3
@olgabot olgabot force-pushed the remove_repetitive_regions_paired_end branch from 7275149 to 912eda3 Compare March 6, 2015 18:19
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olgabot commented Mar 6, 2015

just rebased

@olgabot
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olgabot commented Mar 6, 2015

I'll try doing a merge ...

@olgabot olgabot merged commit 912eda3 into master Mar 6, 2015
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olgabot commented Mar 6, 2015

caveat: the paired end stringent jobs using trimgalore doesn't map with STAR as the single end no trimgalore one does

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2 participants
@olgabot @gpratt