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  • trim adapter from Illumina Genome Analyzer IIe miRNA reads

    Hi everybody,

    I can't find the sequence of the adapter from Illumina's Genome Analyzer II. I've received reads ( 36 nt each sequence ) to detect new miRNA from an ovin model.

    I've found the function trimLRPatterns in R but I need the sequence to trim.

    Can someone help me

    Thanks a lot,

    N.

  • #2
    nobody knows ?

    it will help me a lot.

    Thanks

    Comment


    • #3
      Originally posted by NicoBxl View Post
      nobody knows ?

      it will help me a lot.

      Thanks
      You can try clipRead program at our deepBase database ( http://deepbase.sysu.edu.cn/ ), which were developed to discover small and long ncRNAs from deep-sequencing data.

      you can download clipRead program at http://deepbase.sysu.edu.cn/clipRead/. More detailed information, please see the readme file ( http://deepbase.sysu.edu.cn/clipRead/readme.txt ).
      Last edited by yjhua2110; 08-09-2010, 07:47 AM.

      Comment


      • #4
        See
        http://seqanswers.com/forums/showthread.php?t=198&highlight=sticky


        It should be a sticky but doesn't "stick" to the top

        Comment


        • #5
          thanks, I found the adapter I expect

          3'RNA adapter : UCGUAUGCCGUCUUCUGCUUGU

          In my fastq file, I've got about 19M reads. When I sort the reads on the number of occurences, I found that the sequence with the most important occurence is :

          adapter

          TCGTATGCCGTCTTCTGCTTGTAAAAAAAAAAAAAA (I remplace U by T)

          and the next sequence in the list are similar (It seems that one mismatch appears in the 3! part of the reads )

          I found some other reads with high occurence like that :

          adapter in green and a mismatch in the adapter seq in red

          TCGTATGCCGTCTTCTGCTTGTAAAAAAAAAAAAAA

          and even ( just a part of the adapter is present, the N represent an non-readable nucleotide )

          AGTACAGTCTCGTATGCCGTCTNNNNNNNNN

          the last example appears even with mismatches.

          what is the best method to trim this adapter ?

          Thanks

          Comment


          • #6
            hellö, I have the same problem now, then how did you deal with finally?

            Comment

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