Hi Simon,

I have a query regarding count based method to find differential expression.

As in seqanswers you stated that HTSeq is not for isoform level count as
most of the reads are overlapping, so a major portion of data will be
reagrded as ambigous.

But if instead of rejecting overlapping reads if I assign them to all
isoforms in which they are falling i.e. by using featurecounts and then
find differential expression using DESeq. Do you think the results which I
got after it will be significant?

Please reply.

Regards,
Gourja

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