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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Large number of unmapped reads #57

Open amwa opened 3 years ago

amwa commented 3 years ago

Hi! Another question: in running squire Map on my paired-end RNA-Seq data, I'm getting a really large number of reads classified as Unmapped (about 70%, with 30% falling under "Unmapped other"). Is this expected? What are the possible reasons for these results, and how can I adjust?

The command I'm running is squire Map -1 $read1 -2 $read2 -f $squire_fetch -r $read_length -b hg19 -p 8 -v

Thanks!

rpg18 commented 3 years ago

Hi, Have you checked the main mapping script Map.py? You'll see that squire Map uses STAR, so you may check both STAR documentation and squire's scripts, or go back to the preprocessing of your raw reads. Cheers