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