Recovery of intronic coordinates after CLIPSeq analysis

Pipelines CLIP
1

Hello,

I run a CLIPSeq analysis on PARiCLIP data and started working with one of the output file named:

Curated Data
Normalised genome crosslink bedgraph
Genomic crosslinks normalised to total sample crosslinks in bedgraph format for genome browser viewing.
ctr_R1.norm.transcript.cmd.bedgraph

Its formet is
ENST00000006724 694 695 -1.45098
ENST00000006724 1510 1511 -1.45098

from which I can retrieve the exon information but I miss how to get access to the CLIP tags in introns? Is there any other file I should consider?
Thanks, Best,
Sophie

2

Hi Sophie

You are looking at the transcriptome coordinates as you rightly notice - the genomic mapping/coordinates are found in the files with “genome” in the title.

You might also be interested in the summary files which summarise crosslinks over different genomic regions for you.

Best wishes,
Charlotte