Hi Shamsher,

Another alternative is to use bamqc from the qualimap suite. The wrapper you 
can find at:

You need to install this tool in a local Galaxy, with the qualimap suite 
installed and perl (see README).


On 09/04/2013 09:59 PM, shamsher jagat wrote:

I am looking for a tool to perform QC of Bam file especially following
1. BAsic information and stat.
2. Coverage across reference features- gene/ transcripts.
Is it possible to do it in Galaxy?

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team

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