Small RNA/rRNA/tRNA

Pipelines CLIP
1

Hi Flow team,

I would like to be able to take the smRNA aligned (including rRNA and tRNA) reads from a CLIP analysis and visualise them in a genome browser (UCSC). I was wondering if the Homo_sapiens.GRCh38.109.gtf used contains annotation for this?

Thank you!

Fiona

2

Hiya, it doesn’t you’ll need to download the small RNA fasta that will be linked in the prepare genome run you used to run the clip pipeline. each RNA will be a separate chromosome in IGV!

3

Great thank you, will try to do this now, Fiona