Hi all,
We’ve released a new version of CLIP-Seq pipeline v1.4. This fixes an error in iCount summary files when using newer genome annotations. Previously transcripts were being incorrectly filtered from genes due to a change in the formatting of Ensembl GTF files. If you previously ran your CLIP data with older pipeline versions on the latest genome annotations then your iCount summary files may have had a higher proportion of “intergenic” reads than expected, please do run with the new 1.4 genome versions to get the most accurate summary results.
Please note, we have already generated these for human and mouse, so no need to run the ‘prepare genome’ pipeline yourself for these species.
All best,
Charlotte