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  • bowtie error

    hi all,

    I am trying to use Bowtie to align paired end sequencing data from solexa, I made indexfiles, and run bowtie for my files by this command:

    bowtie -S -a -v 3 -q -I 0 - X 400 -t /mgs/.../Assembled_chromosomes/renames/Allchro -1 /mgs/.../Sequences_original_08-09/s_1_1_sequence.txt -2 /mgs/.../Sequences_original_08-09/s_1_2_sequence.txt s_1_bowt.sam

    read length=101, size of fragment=400bp

    but I am consistently getting this:

    Extra parameter(s) specified: "400", "/mgs/....../renames/Allchro", "s_1_seq_pe_bowt_101_3mis.sam"
    Note that if <mates> files are specified using -1/-2, a <singles> file cannot
    also be specified. Please run bowtie separately for mates and singles.
    Overall time: 00:00:00

    Does anyone have any ideas as to what I should do?
    Last edited by jamal; 10-06-2010, 06:27 AM.

  • #2
    i used bowtie
    and all i used in my query was a .txt file (that was fastq result) and then the indexes that i downloaded from the site

    bowtie -S mm9 ../100920_s_1_seq_GLJ-1.txt mm9_snp_1_1.sam

    like this
    were -S specifice that i use samtools and mm9 = my indexfiles and the txt file is my fastq file and the .sam = output

    Comment


    • #3
      Originally posted by jamal View Post
      hi all,

      bowtie -S -a -v 3 -q -I 0 - X 400 -t /mgs/.../Assembled_chromosomes/renames/Allchro -1 /mgs/.../Sequences_original_08-09/s_1_1_sequence.txt -2 /mgs/.../Sequences_original_08-09/s_1_2_sequence.txt s_1_bowt.sam

      Extra parameter(s) specified: "400",
      Hi Jamal,

      Looks like there's a space between "-" and "X" in the "- X 400" part of your command. If you remove the space ("-X 400"), I think the command should work.

      Thanks,
      Ben

      Comment


      • #4
        Originally posted by Ben Langmead View Post
        Hi Jamal,

        Looks like there's a space between "-" and "X" in the "- X 400" part of your command. If you remove the space ("-X 400"), I think the command should work.

        Thanks,
        Ben
        Thank you Ben.
        I also put my index in current directory , and it worked.
        thanks again.

        Comment

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