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

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?

next-gen genome sequence
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updated by Biostar Biostar • written by mangfu100 mangfu100

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.

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updated by Ram Ram • written by iraun iraun

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.

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written by mangfu100 mangfu100

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

samstat <file.bam>
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updated by Ram Ram • written by iraun iraun

Yes I corrected my fault. Thanks a lot:)

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updated by Ram Ram • written by mangfu100 mangfu100

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

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written by ana_mt93 • ana_mt93

1 answer

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

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updated by Ram Ram • written by Manvendra Singh Manvendra Singh

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