Online tools to generate count tables from sam/bam files

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Does Galaxy or any other online tools offer methods to generate a count table from bam or sam files?

[GenoMax]

Are you trying to get genome-wide coverage or just counts for features (e.g. exons, genes)?

In case of latter, you can use featureCounts ( http://bioinf.wehi.edu.au/featureCounts/), HT-seq (http://www-huber.embl.de/users/ander...doc/count.html).

For the former BEDTools are your best bet. Find a friend who has Xcode installed and get him/her to compile BEDTools for you.

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Thanks, GenoMax. I did get htseq-count from a friend, as it is installed on his server. However, upon running the command

htseq-count -s no -a 0 FourA.sam hg19.gtf > FourA.count

I get zero counts for everything, regardless of whether -s is yes or no, and whether -a is values between 0 and 10.

I am opening up a thread for it. Thanks for help again...

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The other thread is located here:

http://seqanswers.com/forums/showthread.php?t=43056

I just don't know if this is something that can be fixed in a timely manner

[maubp]

Does Galaxy or any other online tools offer methods to generate a count table from bam or sam files?

Yes, I wrapped samtools idxstats for Galaxy, which does that:

http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats

(Although perhaps you are looking for a more detailed count table?)