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  • Bowtie2

    Hello,

    I tried to work with bowtie2 under Linux, but I faced many problems:
    1- The command (bowtie2) is not working as it's written in the manual of Bowtie 2 package but normal commands as bowtie and bowtie build are working.
    2- the example which is with the package lambda_virus , the basename is not recognized although the index files have this basename, so no alignment is allowed, I tried to build other indexes for other genome and set new basename by bowtie builder, but again the new basename is not recognized by bowtie2
    I use the same commands with bowtie1 without any problems so far.

    Thanks,
    Layal

  • #2
    bowtie isn't a normal command with bowtie2. Are you keeping bowtie in your PATH along with bowtie2?

    If you build your ebwt in the /examples/reference directory
    Code:
    bowtie2-build lambda_virus.fa lambda_virus
    Then run the example in the reference directory
    Code:
    bowtie2 -x lambda_virus -U ../reads/reads_1.fq -S eg1.sam
    Output is:

    10000 reads; of these:
    10000 (100.00%) were unpaired; of these:
    596 (5.96%) aligned 0 times
    9404 (94.04%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
    94.04% overall alignment rate
    Did you use bowtie-build or bowtie2-build? Don't have a copy of bowtie anymore (switched over to bowtie2), so I can't say if bowtie and bowtie2 indexes are compatible. Pretty sure they aren't, but I can't test it in front of me.

    If you built with bowtie-build instead of bowtie2-build, it /might/ be the problem.

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