Entering edit mode
2.3 years ago
demoraesdiogo2017 ▴ 90
I have about 12 samples I aligned with mm39. All samples had good quality reads and all paired, as trimmomatic gave me empty files for unpaired reads. Strangely, two of them had 0% alignment with the genome. I blasted a few reads and they seem to match mus musculus or other rodents. I'm using HISAT2 on galaxy. Is it a bug?
sure I will delete the post here and post there
I have undeleted the post so that others can see what the right course of action is if they have similar questions.