How to identify index sequences for cutadapt for atac-seq

Question

I am just starting on my atac-seq analysis (not very experienced, so my apologies for a stupid question), and I am wanting to trim the adapters of off my paired-end reads.

I am following the galaxy atac-seq protocol that says to enter in the custom 3' adapter sequence. I took the primer sequences from Buenrostro.

>Ad1_noMX
AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG
>Ad2.7_CTCTCTAC
CAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGGAGATGT

Following the ATAC protocol, I see that the primer sequences they used are the reverse complement sequences of the end of the provided sequences (ACATCTCCGAGCCCACGAGAC/CACATCTGACGCTGCCGACGA). I took this part and added the reverse complement index primer of 2.7 (GTAGAGAG) to the front.

So for my R1 my sequence is: GTAGAGAGACATCTCCGAGCCCACGAGAC And for my R2 my sequence is: GTAGAGAGCACATCTGACGCTGCCGACGA

However, when I run the command I only get 1.4% read1/2 with adapter. Could anyone suggest where I am going wrong?

Thank you

Answer 1

The sequence to trim for ATAC-seq is CTGTCTCTTATACACATCT. It's the Nextera adapter sequence. The sequence is the reverse complement of the 3' ends of your primers, both forward and reverse.

You trim adapters which come before any index sequence so trimming adapter (and by this everything beyond it) is sufficient.