Problem in file.res.out : dat.pos empty

[stoumoi]

Dear all,

I try to use GIREMI on my RNAseq data with the simple command :

giremi -f genome.fasta -l panel.txt -o file.res A11_aligned_sort.bam

and I have always the same error :

cbind(dat.pos[,c("upstream_1base","downstream_1base")],abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1) Erreur dans data.frame(..., check.names = FALSE) : les arguments impliquent des nombres de lignes différents : 0, 1 Calls: cbind -> cbind -> data.frame Exécution arrêtée

I understand than the table dat.pos in giremi.r is empty because i have a problem at the line : dat[rownames(subset(dat,pvalue_MI>0 & pvalue_MI <= 0.05)),"ifRNAE"]= 1 -> But I don't have lines with the condition : pvalue_MI>0 & pvalue_MI <= 0.05...

The two values on screen "meanMI" and "sdMI" seem correct : meanMI:0.107369 sdMI:0.239185

Is it possible that this is a problem with the coverage in my bam file ?

Best, Stephanie

[zhqingit]

Hi Stephanie,

I guess all the sites in your SNV list can't pass the MI test. Could you send me the two values on the screen: meanMI and sdMI when you run giremi?

Best, Qing

2016-05-11 6:42 GMT-07:00 stoumoi notifications@github.com:

Dear all,

I try to use GIREMI on my RNAseq data with the simple command :

giremi -f genome.fasta -l panel.txt -o file.res A11_aligned_sort.bam

and I have always the same error :

cbind(dat.pos[,c("upstream_1base","downstream_1base")],abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1) Erreur dans data.frame(..., check.names = FALSE) : les arguments impliquent des nombres de lignes différents : 0, 1 Calls: cbind -> cbind -> data.frame Exécution arrêtée

I understand than the table dat.pos in giremi.r is empty because i have a problem at the line : dat[rownames(subset(dat,pvalue_MI>0 & pvalue_MI <= 0.05)),"ifRNAE"]= 1 -> But I don't have lines with the condition : pvalue_MI>0 & pvalue_MI <= 0.05...

Is it possible that this is a problem with the coverage in my bam file ?

Best, Stephanie

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/15

[stoumoi]

Hi Qing,

The two values on screen "meanMI" and "sdMI" seem correct : meanMI:0.107369 sdMI:0.239185

In fact, my SNV list is extract from a public database. I checked my fasta file and remove the N positions in my list. Here is the header : chr1 14603 14604 rs541940975 1 + chr1 15117 15118 rs11580262 1 + chr1 15776 15777 rs568149713 1 + chr1 17221 17222 rs200978805 1 +

Thanks, Stephanie

[zhqingit]

Hi Stephanie,

In theory, the meanMI should be about 0.7. The value 0.1 means many sequencing errors or RNA editing sites are marked as SNP. So I suggested you can use more stringent SNV calling methods.

Best, Qing

2016-05-18 1:57 GMT-07:00 stoumoi notifications@github.com:

Hi Qing,

The two values on screen "meanMI" and "sdMI" seem correct : meanMI:0.107369 sdMI:0.239185

In fact, my SNV list is extract from a public database. I checked my fasta file and remove the N positions in my list. Here is the header : chr1 14603 14604 rs541940975 1 + chr1 15117 15118 rs11580262 1 + chr1 15776 15777 rs568149713 1 + chr1 17221 17222 rs200978805 1 +

Thanks, Stephanie

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/15#issuecomment-219966348

[stoumoi]

Hi Qing,

Thank you very much for your help ! Indeed, my SNV file is extract from dbSNP... I will try to filtre my file. Do you propose an other database to extract SNV for Human (GRCh37) ?

Best, Stephanie

[zhqingit]

Hi Stephanie,

dbSNP is fine. I mean some SNV sites called by your SNV calling method might be the sequencing error. And these error sites have been marked as the SNPs based on the dbSNP, which can cause the MI values small. So my suggestion is to use more stringent SNV calling method or parameters.

Best, Qing

2016-05-19 2:07 GMT-07:00 stoumoi notifications@github.com:

Hi Qing,

Thank you very much for your help ! Indeed, my SVN file is extract from dbSNP... I will try to filtre my SNV file. Do you propose an other database to extract SNV for Human (GRCh37) ?

Best, Stephanie

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/15#issuecomment-220268576