Entering edit mode
7.8 years ago
linaskunigenas
•
0
Hello.
I tried to align miRNA seq data to mirBase mature and hairpin RNAs with bowtie and bowtie2 and got very low alignment. I tried some experiments aligning sequences from reference file and it seems that the problem is that mature mirnas from mirBAse are 5>3 RNAs while my Reads are 3>5 cDNAs. Could this be a problem? If it is, building index from mature.gff3 file could help, however i cannot find how to do it.
Thanks.
