filter transcript isoforms with low support

Question

[ignazio.fontana]

Hi, I need to filter transcript isoforms of my de novo assembled transcriptome with low support by removing isoforms minor of a percentual of the Trinity gene subcomponent read support. (in my case 0.01%) What is the correct strategy? I never made that. Thanks

Answer 1

[Kristoffer Vitting-Seerup]

It's quite common to filter transcripts on both expression (read counts) and the isoform fraction (fraction of gene expression originating from each isoform) so sounds like a good plan. Just make sure that you calculate your gene expression before doing that filtering (aka the transcript removal should not effect the gene expression).

[ignazio.fontana]

Thanks a lot. Can you indicate to me some software to do it?