Hello!
I am using Galaxy. I have a library of small RNA in FASTQ format that I am trying to filter by size. The file has around 38,000,000 reads and is 5.5GB. The Galaxy tool I used was "Filter FASTQ reads by quality score and length". I want to discard all reads that fall outside the range of 19-25 bases long.
This is my first time using the tool, but I'm fairly sure I have input the few simple parameters correctly. I have tried restarting the job a few times and have left one attempt going for 24 hours+. It takes a couple minutes to move from grey (in queue) to yellow (in progress), but stays on that stage for hours and never completes.
Is this usual behaviour? Anything I can do to troubleshoot? Is there another tool in Galaxy that will filter my FASTQ file by read size?
Thankyou for any suggestions!
If this question is about PSU galaxy then it is better suited to be posted over at Galaxy biostar.