hi All,
I am very new to this NGS business.. Presently I am trying my hands on RNA-seq data. I have managed to obtain the SAM files by running topHat.
I also ran cufflinks on those files. I now want to conduct differential expression analysis using DESeq package. (and eventually compare the results of cufflinks and DESeq). How do I obtain the raw read counts from the SAM file? I read that that is the input to DESeq. Can someone please help?
thanks.
I am very new to this NGS business.. Presently I am trying my hands on RNA-seq data. I have managed to obtain the SAM files by running topHat.
I also ran cufflinks on those files. I now want to conduct differential expression analysis using DESeq package. (and eventually compare the results of cufflinks and DESeq). How do I obtain the raw read counts from the SAM file? I read that that is the input to DESeq. Can someone please help?
thanks.
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