Stuck at adapter trimming

[HarshJ]

Hi!

So, I'm trying to analyse and subsequently map the data deposited with the following paper:

http://science.sciencemag.org/content/354/6313/aah5651.full

I have downloaded and 'fastq-dump'ed the ChIP-Seq files and have also run a fastqc for quality scores. Now as these reads are raw, they still need adapter trimming and filtering. However, I am unable to figure out what adapter sequence to use for trimming.

I am putting up this question here because the paper states,

Libraries for ChIP-seq were constructed using the NEBNext ChIP-seq kit (New England Biolabs), barcoded, multiplexed, and sequenced on an Illumina MiSeq with a paired-end run type

Help!

[GenoMax]

You can find the NEBnext adapter sequences in this manual.

[fkrueger]

You should be able to use Trim Galore for this which will try to identify the adapter sequence for you. The command for adapter and quality trimming is simply:

trim_galore --paired file1 file2