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  • Best way to trim MiSeq - NEBNext Multiplex Oligos for Illumina Library

    I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.

    The sample sheet looks like this:

    Code:
    IEMFileVersion,4
    Investigator Name,FB
    Experiment Name,WT10104
    Date,11/27/2013
    Workflow,GenerateFASTQ
    Application,FASTQ Only
    Assay,TruSeq Small RNA
    Description,
    Chemistry,Default
    
    [Reads]
    51
    
    [Settings]
    ReverseComplement,0
    
    [Data]
    Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
    HS130333-1,,,,RPI3,TTAGGC,,
    HS130333-2,,,,RPI4,TGACCA,,
    HS130333-3,,,,RPI5,ACAGTG,,
    The Primer index manual can be found here.

    Sor for HS130333-1 file, according to the manual above the primer/adapter with index is:
    5 ́-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́

    The document indicated that the expected index primer sequence read is TTAGGC which is the reverse complement of GCCTAA.


    My question is if I use `trim_galore` or `cutadapt` to trim the data, what is the parameter -a I should use?

    Is it the whole sequence above? Or first 5 ́-CAAGCAGAAGACGGCATACGAGAT?
    Or GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3 ́? (and what is 's' means here)

    Or the reverse complement of the each of above?
    Last edited by foolishbrat; 01-26-2014, 10:33 PM.

  • #2
    Cross-posted and solved: http://seqanswers.com/forums/showthread.php?t=40290

    Comment

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