Question: ChIPQC 0 unmapped does not agree with the samtool generated stats
0
gravatar for ew152
22 months ago by
ew1520
ew1520 wrote:

Hi,

I apologize if I missed this question somewhere.

I am new to the ChIPQC package. When I put my bam file into the ChIPQC, it always gives me unmapped read =0. I know this is not the case as the bam file is simply generated by samtools sort. If I feed this bam file to samtools idxstats, it will give certain number of unmapped reads. 

I tried this in single sample in ChIPQCsample(bam, peak) as well as in group in ChIPQC(experiment,annotation="hg19", chromosomes = NULL) but the unmapped read is always 0. Is there anything I did wrong? Thank you!

test = ChIPQCsample("bam/LW-L1_S1_L004.marked.bam", peaks="macs2/LW-L1_S1_L004_peaks.broadPeak")
QCmetrics(test)
flagtagcounts(test)

> QCmetrics(test)
       Reads         Map%        Filt%         Dup%        ReadL        FragL 
29479443.000      100.000       26.200       87.100       50.000      105.000 
       RelCC          SSD         RiP% 
      -0.104        5.520       16.800 
> flagtagcounts(test)
         UnMapped            Mapped        Duplicates          MapQPass 
                0          29479443          26274707          21742611 
   MapQPassAndDup DuplicateByChIPQC 
         18946647            320941 

chipqc • 285 views
ADD COMMENTlink written 22 months ago by ew1520
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 285 users visited in the last hour