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  • Multiple index files in Bowtie?

    Hello Everyone,

    I am working on a 32 bit RH Linux machine and setting up a RNASeq analysis pipeline. As part of ERANGE, I am building an index of the expanded genome but on including .fa.masked files the total number of characters balloons to more than 2^32. I went ahead and built two index files by splitting all the files into two sets.
    I tried an small example of aligning a 36bp read against both the refseq and ensembl index. No alignments are found if I use two index together in the command line but they are found when searched against one index at a time. Is this the only option when there are multiple index files or am I missing something more obvious?

    Thanks for your help.

  • #2
    I run an RNAseq pipeline where we sequentially align against two different indexes, maybe I can help. can you copy/paste the commands you use, also listing any options?

    Comment


    • #3
      for eg. I want to align CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA against two index files hg18_block1 and hg18_block2. Since I am still building the index, I will give an example using different index

      $bowtie -t human_ensembl_cdna -c CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA
      Time loading forward index: 00:00:01
      Time loading mirror index: 00:00:02
      Seeded quality full-index search: 00:00:00
      0 + ENST00000322310 755 CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 7:T>C,18:C>N
      Reported 1 alignments to 1 output stream(s)
      Time searching: 00:00:03
      Overall time: 00:00:03

      $bowtie -t refseq_human -c CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA
      Time loading forward index: 00:00:02
      Time loading mirror index: 00:00:01
      Seeded quality full-index search: 00:00:00
      0 + REFSEQ:NM_003731 800 CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 7:T>C,18:C>N
      Reported 1 alignments to 1 output stream(s)
      Time searching: 00:00:03
      Overall time: 00:00:03

      The following does not work:
      $bowtie -t human_ensembl_cdna -t refseq_human -c CCCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA
      Time loading forward index: 00:00:02
      Time loading mirror index: 00:00:01
      Seeded quality full-index search: 00:00:00
      No results
      Time searching: 00:00:03
      Overall time: 00:00:03

      Is a sequential search the only option or is there a way to do alignment against multiple index files simultaneously.

      Thanks.

      Comment


      • #4
        unfortunately, sequential is the only way to do it as far as I know.

        Comment

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