search

mourisl / Rcorrector

Error correction for Illumina RNA-seq reads
GNU General Public License v3.0
62 stars 18 forks source link

Suggestion: not discard unpaired and unfixable in filter script #13

Closed sandbardev closed 5 years ago

sandbardev commented 5 years ago

Hello. I'd like to make a suggestion. It'd be extremely useful to not discard the unpaired reads after filtering in order to determine DEG. Right now your filter script completely removes both unfixable and unpaired reads.

What'd be the best way to configure this in the script myself, if needed? I'd like to have three outputs: fixed*, removed*, and unfixable_*.

mourisl commented 5 years ago

Rcorrector does not discard any reads and there is no filter script in Rcorrector. Is this from other sources?

sandbardev commented 5 years ago

Apologies. We have been using a filter script that separates the reads as described above. I had been told that it came alongside rcorrector, so much that my teacher mentioned it was weird for the script to not be an integral part of rcorrector itself. This is the actual source of the filter script I mentioned: https://informatics.fas.harvard.edu/best-practices-for-de-novo-transcriptome-assembly-with-trinity.html

Once again, apologies. I will close the issue now.