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  • Cut the reads.. paired end fastq file

    hi.. i have the following 150bp reads.. i would like to cut the bases which are more than 100bp. Also i would like to cut from begining of the read. please let me know any script or program which can do this.

    Code:
    @HWI-DO4456:7:000000000-Z07CL:1:1:15052:1479 1:N:0:GGCTAC
    TCCTCAGATTTTTTAGAAAGAGGAGTCTGCTTATAAGATAATGGCATCATTTTGATAGAATCTCCTCGCATTGTTGTAAAACTAATAACAAAGAAGGTTGGTTTTTGTGGTTTTGGTCTCCCGGCCTGAATCCAAGCTTGATGAATACGAA
    +
    @CCFFFFFHHHHHJJIJJJJJJIJJJJJJJJJIJJJIJJJIJJJJJJJJJJJJIJJJJJJIJGJJJJJJFHHFFFFFEEEEDEDDDDDDDCDDCBDD>@CB?BDDDDDDDCBDDDBBCDDDDDDDBDDDDDDDDDCBCDCBCDDDDEDDDD
    @HWI-D04456:7:000000000-Z07CL:1:1:17590:1511 1:N:0:GGCTAC
    TTAATTATACTTGTTGGTTTTGGTGGCGGATTAACATGGGGAGCAGTCGCTCTTCGTTGGGGTAAATAAGGACTGAGAGAAAAAAAGGAGTGTATTTTGTGAAGGTAGGGGCACAGTACCGTTGAAGCGTCTAATGAACGTGGAGGGATGG
    +

  • #2
    Do you mean keep the left end, or keep the right end?

    What is your favourite scripting language (since there are lots of options here, Perl, Python, Ruby, etc)?

    Comment


    • #3
      i use perl.. keep the right end.. and trim the left end.. i already trimmed adapters..

      Comment


      • #4
        perl is OK
        fastx_trimmer provided by FASTX_Toolkit may be faster.

        Comment


        • #5
          I recently used fastx_trimmer on my data and I can only recommend it.

          Comment


          • #6
            hello i am new member beginner to the field

            Comment

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