Entering edit mode
8.4 years ago
mangfu100 ▴ 800
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?
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.
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.
Yes, I use it very often. The output file is a html page. What is the command you used?
Yes I corrected my fault. Thanks a lot:)
Hello, I have the same problem that you did: output results size 0. Could you tell me how did yo fix it?