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  • Stuck at adapter trimming

    Hi!

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



    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!

  • #2
    You can find the NEBnext adapter sequences in this manual.

    Comment


    • #3
      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:

      Code:
      trim_galore --paired file1 file2

      Comment

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