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  • dicty
    Member
    • Nov 2010
    • 28

    Bowtie and samtools questions

    I'm new in sequencing analysis and have a couple of questions to ask.

    1. I’m trying to use bowtie-inspect to reconstruct fasta file from the BOWTIE index, but couldn’t get anything. I’m using 12.7 version.

    Here is the command:
    ./bowtie-inspect e_coli

    Then I got the following output, but nothing else:
    Command: ./bowtie-inspect e_coli

    Why I cannot run bowtie-inspect? Is there anything wrong?

    2. I installed samtools and try to produce a .fai file with "samtools faidx", but I got the following errors.

    ./samtools: No such file or directory
    or
    samtools: command not found

    How do I run samtools? Is there anything wrong I did?

    Thanks a lot!

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