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  • arcolombo698
    Senior Member
    • Nov 2013
    • 142
    #1

    ILLUMINACLIP adapter.fa file creation

    Hello.

    I am using trimmomatic and know that the sequences to be removed are

    Adapter 5’ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
    >>TruSeq Adapter, Index 1
    >>5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
    >>TruSeq Adapter, Index 2
    >>5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
    >>TruSeq Adapter, Index 3
    >>5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG


    however I do not know how to create the adapter.fa file knowing just the sequence names.

    Could anyone provide a sample adapter.fa file that they use as a adapter reference for trimming using the command ILLUMINACLIP ?

    my other option is to use adaptercut, but I want to try the reference adapter.fa first...seems easier
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      see the answer in: http://seqanswers.com/forums/showpos...20&postcount=7

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