auto trimming of adapter and 6 base normalizing sequence from miRNA reads

Question

[Richard]

Hi all,

Apologies if my terminology isn't correct on this one...

I'm used to looking at microRNA reads from which I need to trim some amount of adapter off the ends. I have a simple script to take care of this that works relatively well. However, I'm starting to look at microRNA data from a different protocol where the reads are longer (good for identifying adapter) but there is also a 6 base "stuffer"* sequence inserted before the adapter that is introduced with the intention of reducing the selection bias in library construction. I think there should be tens of unique "stuffer" sequences in any one library.

EDIT

Contrary to what I posted earlier, the stuffer sequences are random. So now, this really boils down to finding a tool that can trim the adapter and then trim 6 bases off after that. I'll try out trimgalore, cutadapt and others to see what works best.

*stuffer probably isn't the right word, but I can't recall the precise term.

[hxlei613]

How do you figure it out ? I'm facing with the same problem.

[Brian Bushnell]

bbduk.sh in=reads.fq out=trimmed.fq ref=adapters.fa ktrim=r k=23 mink=9 hdist=1 trimpad=6

The trimpad=6 will trim 6 extra bp when adapters are detected.

[GenoMax]

bbduk.sh is part of BBMap suite.

Answer 1

[Brian Bushnell]

BBDuk will trim adapter sequences on either the left or right side, given a set of sequences. The exact command depends on the orientation of the adapters. Can you draw a diagram of what they look like? I'm imagining something like this, in a sequenced read:

[6-8bp of spacer][15+ bp of genomic DNA][Read2 adapter readthrough]

Is that correct?