RNA-seq data QC

Aishah · 08-08-2019, 02:00 AM

Regarding trimming of raw RNA-seq datasets, do we need to trim off primer sequences despite FASTQC not indicating these as overrepresented?

GenoMax · 08-08-2019, 04:17 AM

I assume you are referring to adapter sequences. Strictly speaking you don't need to since most modern aligners will soft clip them.

That said, it can be a good practice to scan and trim your data so you can be sure that there is no extraneous sequence present.

08-08-2019, 02:00 AM	#1
Aishah Junior Member Location: Mauritius Join Date: Aug 2019 Posts: 3	RNA-seq data QC Regarding trimming of raw RNA-seq datasets, do we need to trim off primer sequences despite FASTQC not indicating these as overrepresented?

08-08-2019, 04:17 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,994	I assume you are referring to adapter sequences. Strictly speaking you don't need to since most modern aligners will soft clip them. That said, it can be a good practice to scan and trim your data so you can be sure that there is no extraneous sequence present.