Isoform level RNA-seq analyses
Hi,
I am considering to filter my transcripts based on expression, in that case, what are the options to choose the highly expressed isoform of each gene in a count matrix ( for example, salmon or FeatureCounts)?
I found out that trinity has an option of isoform level filtering ( via its filter_low_expr_transcripts.pl ), but I was wondering, if there are other options you know of & trust in your analyses?
Thank you!
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What is the analysis goal? Why do you want to filter?
I would like to keep the isoforms which are always being expressed regardless of the condition, so that I can use them in other analyses, for ex. checking how translation is effected etc.