Hi, I have 6 couples of paired end libraries (rnaseq) from Novaseq 6000. It is the first time I work with this kind of data; I read the header of my fastq and they have a double index. What software can I use to trimming adapters? Can I use trimmomatic and what adapters reference file I have to use? Thanks Ezio
Can I use trimmomatic and what adapters reference file I have to use?
Yes, you can use any trimming software. Besides
bbduk.sh from BBMap suite is an easy option. BBMap distribution includes a file which contains adapter sequences for most commonly used Illumina kits (
resources directory when you download the software).
BBMap suite also has another tool called
clumpify.sh which you may want to look at to see what kind of duplicates (all, optical) your data has since this is a patterned flowcell (A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files )