STAR,HTseq-DEseq2/edgeR for DE,SNPs etc

Question

[justinfanyi]

I have RNAseq paired end illumina reads from 6 control and 6 treatment samples, I would like to validate DE results I got from this pipeline: Bowtie-Tophat-cufflinks-cuffmerge-cuffquant-cuffdiff-cummeRbund. Eventually do other analysis like SNP calling etc.

Any recommendation on the above stated set or any other ideas to validate the results

Thanks.

Answer 1

[Devon Ryan]

Using STAR and DESeq2 would allow you to determine which results are program specific, but I would in no way consider this to be validation. I would encourage you to validate candidates in additional samples with qPCR or similar.

Answer 2

[justinfanyi]

Thanks Ryan!