Segmentation fault

[IraShch]

Hello Qing,

I can't start Giremi due to segmentation fault occurring at the very beginning of the run.
My command is following:
./giremi -f /home/schukinai/research/hg19.fa -l ENCFF001SGE.fixed.M.grm -o giremi_K562_test.res /Johnny/shchukinai/ENCFF001SGE.purified.fixed.bam
SNV file is attached.

Could you help me with this problem? Thank you!

Best,
Ira

ENCFF001SGE.fixed.M.txt

[zhqingit]

Hi Ira,

The last column should be '#','+' or '-'.

Best,
Qing

2016-05-01 15:03 GMT-07:00 IraShch notifications@github.com:

Hello Qing,

I can't start Giremi due to segmentation fault occurring at the very
beginning of the run.
My command is following:
./giremi -f /home/schukinai/research/hg19.fa -l ENCFF001SGE.fixed.M.grm -o
giremi_K562_test.res /Johnny/shchukinai/ENCFF001SGE.purified.fixed.bam
SNV file is attached.

Could you help me with this problem? Thank you!

Best,
Ira

ENCFF001SGE.fixed.M.txt
https://github.com/zhqingit/giremi/files/244360/ENCFF001SGE.fixed.M.txt

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub
#14

[IraShch]

Hi Qing,

Thank you for your help!
I managed to run Giremi, but not the following R script. As far as I understood the problem is that there are no positions with significant p-values (mip > 0 && mip < 0.05).
Could you, please, recommend conditions (maybe some parameters to pass) which will help to increase Giremi's sensitivity? Or is it only about my data?

Best,
Ira

[zhqingit]

Hi Ira,

Yes, actually you can increase the mip values to get more positions, such
as mip<=0.1, for the model training. But before do that, I'd like to see
your output from the girmie. And giremi will print two values on screen
"meanMI" and "sdMI" when you run it, so I wonder if you can send me the two
values and I can do more evaluation.

Best,
Qing

2016-05-02 13:26 GMT-07:00 Ira Shchukina notifications@github.com:

Hi Qing,

Thank you for your help!
I managed to run Giremi, but not the following R script. As far as I
understood the problem is that there are no positions with significant
p-values (mip > 0 && mip < 0.05).
Could you, please, recommend conditions (maybe some parameters to pass)
which will help to increase Giremi's sensitivity? Or is it only about my
data?

Best,
Ira

—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub
#14 (comment)

[IraShch]

I got these values
meanMI:0.006303 sdMI:0.045975

[zhqingit]

Hi Ira,

I guess there are some issues in your SNV list. In theory, the mean of the
MI of SNP pairs should be around 0.69. The 0.006303 means there are many
sequence errors or RNA editing are marked as SNPs. What SNV caling method
did you use?

Best,
Qing

2016-05-03 13:32 GMT-07:00 Ira Shchukina notifications@github.com:

I got these values
meanMI:0.006303 sdMI:0.045975

—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub
#14 (comment)

[IraShch]

Hi Qing,

I used following pipeline:

1. Variant calling by platypus
2. Variant annotation (Ewnsembl VEP)
3. Filtering and formatting of the results

Best,
Ira

[zhqingit]

Hi Ira,

I didn't use platypus. I wonder if you can use more strict parameters to
call the SNVs and run giremi again to see the change of the meanMI.

Best,
Qing

2016-05-03 14:40 GMT-07:00 Ira Shchukina notifications@github.com:

Hi Qing,

I used following pipeline:

1. Variant calling by platypus
2. Variant annotation (Ewnsembl VEP)
3. Filtering and formatting of the results

Best,
Ira

—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub
#14 (comment)

[IraShch]

Thank you for your help!

All the best,
Ira