Does Galaxy or any other online tools offer methods to generate a count table from bam or sam files?
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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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Originally posted by lanner View PostDoes Galaxy or any other online tools offer methods to generate a count table from bam or sam files?
(Although perhaps you are looking for a more detailed count table?)
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