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  • alig
    Member
    • Sep 2008
    • 44
    #1

    trouble getting Bowtie aligner to run

    Hi,

    This is my first time in years I have tried to run Bowtie aligner. I have indexed the reference sequence for colorspace. Now I am trying to align my SOLiD paired end reads. But the program doesn't seem to like my command input. Can anyone help?

    This is what I type in the command line :-

    ../../Bowtie/bowtie-0.12.7/bowtie -C -f -t --ff ../Bowtie_indexes/hg18_noran_mask -1 seqs_F3.csfasta -2 seqs_R3.csfasta --Q1 seqs_F3_QV.qual --Q2 seqs_R3_QV.qual --un seqs_unaligned -al seqs_aligned > seqs_bowtie_map

    Any help would be gratefully received.

    Thanks alig
    Tags: None
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