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  • Do not know Adapters inside Sequences

    I have ~100 Bissulfite-Seq fastq files and ~100 RNA-Seq fastq files representing many samples. All of the seq files were produced by Illumina tech.
    I want to pre-process the fastq files by removing bad-quality base calls and adapters. The problem is that I do not know any adapter used for any of these files.
    My question is: Is there any default adapters for Illumina Seq? I found in the documentation of Trim Galore that the default adapter is (AGATCGGAAGAGC). Shall i use it?

  • #2
    You could use Trimmomatic, it comes with a file of Illumina adapter sequences, though you would have to guess which version of the adapters are used in your data.

    One way to find out which adapters are in your data would be to do 'grep' for the adapter sequence and see how many times it occurs in your data.

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    • #3
      There is a tool called samstats that looks for a very common chain in your sequences. Try to run it and it will show you your adapters sequence

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      • #4
        Thank you very much indeed @mastal and @AJERYC and sorry for late reply.
        I used Trimmomatic and it works fine!

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