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

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[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

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[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

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[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

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[IraShch]

Thank you for your help!

All the best, Ira