Salmon for Nanopore reads

126 views
Skip to first unread message

Nadine Dunn

unread,
Feb 4, 2018, 6:14:26 PM2/4/18
to Sailfish Users Group
Hi all,

Does anyone have experience/opinions on trying the Salmon alignment-based mode with long Nanopore reads? I first aligned my reads against the GENCODE transcripts using minimap2, which includes options for Nanopore RNA-seq. Wondering if there is anything glaringly obvious wrong with this approach?  I had assumed it wouldn't be suitable without some Nanopore-specific option.  I did notice Salmon is only mapping about 15% of the reads compared to minimap2. 

Thanks,
Nadine
Reply all
Reply to author
Forward
0 new messages