On Fri, Sep 6, 2013 at 12:32 AM, Joachim Jacob | VIB | <joachim.jacob@vib.be> wrote:

Hi Shamsher,


Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at:
http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite

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


Cheers,
Joachim

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

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

--

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