I will apologize in advance if this is a really obvious question. I am analyzing some RNA seq data using TopHat/Bowtie for alignment and Cufflinks for expression analysis. I want to pull out the consensus sequence for all the reads that align to a particular gene. I know that I can use SAMtools to pull out all the raw reads that align to a region, but that is still thousands of individual reads to deal with.
Is there a function that I am missing in the software packages I currently use? Or is there some alternative piece of software that I should be using?
Thanks in advance!
Is there a function that I am missing in the software packages I currently use? Or is there some alternative piece of software that I should be using?
Thanks in advance!
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