How to check the bam file of read quality with graphically visual?

Question

[mangfu100]

Hi there.

I have two bam files which followed the preprocessing including GATK.

and I would like to check these two bam files read quality as graph in order to understand easily.

Is any library or program that provides the read quality of these bam files containing with some charts?

[iraun]

Do you mean something like SamStat? It reports all statistics for unmapped, poorly and accurately mapped reads separately of your bam files. Also it is very intuitive and easy to install and understand.

[mangfu100]

DId you use it before?

Now I have used samstat for my bam files. It works, however, it makes output results size 0.

I didn't know where problem occurs.

[iraun]

Yes, I use it very often. The output file is a html page. What is the command you used?

samstat <file.bam>

[mangfu100]

Yes I corrected my fault. Thanks a lot:)

[ana_mt93]

Hello, I have the same problem that you did: output results size 0. Could you tell me how did yo fix it?

Answer 1

[Manvendra Singh]

RSeqQC might help you to get mapping statistics

bam_stat.py -i myFile.bam

for stats in graphical way

qualimap is nice one, you can find it here PS: I have never used it.

for other information this site would be useful for you

http://barcwiki.wi.mit.edu/wiki/SOPs/miningSAMBAM