From the numerous posts here on seqanswers it's becoming increasingly evident that cufflinks and cuffdiff have some major issues relating to calculation of DE significance across multiple samples.
As such we are looking for suitable alternatives for DE calculation of tophat mapped datasets.
There area number of R based software packages available (like edgeR, DEseq, DEGseq) but all these rely on the data being in a count table for input into R.
Can anyone suggest the best/easiest way of transforming the data in .bam files to count tables?
I believe this can be done with HTSeq but are any of you using alternative methods that you can recommend?
Thanks in advance
As such we are looking for suitable alternatives for DE calculation of tophat mapped datasets.
There area number of R based software packages available (like edgeR, DEseq, DEGseq) but all these rely on the data being in a count table for input into R.
Can anyone suggest the best/easiest way of transforming the data in .bam files to count tables?
I believe this can be done with HTSeq but are any of you using alternative methods that you can recommend?
Thanks in advance
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