Library type for Nanopore libraries

COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

https://combine-lab.github.io/salmon

GNU General Public License v3.0

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Library type for Nanopore libraries #211

Open imet-k opened 6 years ago

imet-k commented 6 years ago

I tried to use this tool for Nanopore direct RNA sequencing. However, library type was not recognized.

sdwien commented 5 years ago

I used -l SR (stranded and reverse strand) for nanopore direct RNA Seq data.

callumparr commented 3 years ago

I have used "U" as was default in config.yml for pipeline-transcriptome-de but now I am thinking it should be stranded but i am not understanding the reverse part? Should it not be SF as this is essentially single-read and the baseball sequence is output as 5' to 3' of original RNA molecule despite being sequenced in the reverse from 3' to 5'.