Feature request: Remove unfixable reads

[Shellfishgene]

Hi! It would be nice to have an option to remove unfixable reads (and their pairs) from the output.

[jamlover]

Hi. I don't have anything to do with Rcorrector but here's a link to a few tools including a script that will do what you requested:
https://github.com/harvardinformatics/TranscriptomeAssemblyTools

Specifically you want the script FilterUncorrectabledPEfastq.py

I found the link to the tools while checking this out:
https://informatics.fas.harvard.edu/best-practices-for-de-novo-transcriptome-assembly-with-trinity.html

Perhaps you've already moved on but in case you haven't, hope that helps.

[Shellfishgene]

Thanks, I've already found that one also and have been using it. I just thought that should be easy to implement in Rcorrector so you wouln't have to go through the files twice.

[jamlover]

Agreed.

[mourisl]

Thanks for the suggestions. But I think for the unfixed reads, they might be from low expressed alternative-spliced transcripts. So including this option could make "removing“ be used without caution, and lose some positive reads.