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  • how to get rid of adapter sequences

    Hello,

    I received a dataset of reads that are supposed to have the following format:

    bases (1-3) = 3bp fingerprint (I know what this sequence should be)
    bases 4-28 = 25bp read
    bases 29-36 = 8bp adapter sequence (I know what this sequence should be)

    The fingerprint is OK and the 1st 3 bases where thus trimmed.

    However, in many cases, the adapter sequence is a few bases longer or shorter than 8bp. Thus, trimming 8bases from the end results in reads that lack a few bases or that contain a few bases from the adapter...

    In some reads, I can't find the adapter sequence... it seems like I have 25+8 bases of genomic sequence, but I'm not sure about that...

    Is there a way to qualitatively trim the reads from the end, removing all (but only) the adapter sequence?

    Thanks a lot for your help
    -a-
    Last edited by asheenlevrai; 12-29-2011, 11:49 AM.

  • #2
    What kind of data you've got?

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    • #3
      mRNA 5' end reads

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      • #4
        Free, secure and fast downloads from the largest Open Source applications and software directory - SourceForge.net


        The OSX binaries are posted somewhere here on SEQanswers.
        --------------
        Ethan

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        • #5
          you can use this also
          http://edwards.sdsu.edu/prinseq_beta/

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