RNA-seq quality report sequence duplication level

[rezarahman12]

Hi rMATS team,

I would like to apply rMATS on our recent RNA-seq data. During QC check of the fastq files using FastQC, I see a high level of sequence duplication (please see the attached fig). Do I need to remove it before running rMATS?

I appreciate your time.

Kind regards
Reza

Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

[EricKutschera]

The FastQC plot shows that there is a high level of duplication, but it doesn't give details about the particular sequences. Ideally you could take a look at your files to see what the sequences are. It's possible that the duplicates are due to actual high levels of certain sequences in your samples or it could be due to some technical issue

rMATS should not give any errors related to duplicate sequences. You could try running rMATS and if you get any significant output you can look at those regions in the bam files to see if anything looks unusual