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  • Filtering rRNA out using Bowtie2

    Hello experienced colleagues,
    I'm trying to filter out ribosome-related reads from my Illumina (Casava 1.8) pair-read (100 bp) data. The data was pre-filtered with Trimmomatic (adapters and low quality reads were removed). Now all this stuff exists in 3 files: “left.fq”, “right.fq” and “unpaired.fq”. Ribosome sequences are stored in the bowtie2-build “rRNA” base.

    The simplest story about Bowtie2 syntax is in case of unpaired reads:
    bowtie2 -p 8 --un /output/filt_unpaired.fq rRNA /input/unpaired.fq
    It works.

    But, more dramatic situation arises if I want to get filtered pair-reads in 2 separate files and additionally reads from broken during filtration pairs in a 3-d file.
    I'm trying to do the following:
    bowtie2 -p 8 -X 430 --un-conc /output/filt_pairs.fq rRNA -1 /input/left.fq -2 /input/right.fq
    But, bowtie2 outputs just concordant pairs in 2 files... broken pairs are lost.
    How to get them?

  • #2
    did you find a solution to this problem? I'm going to attempt to trim with trimmomatic and then filter rRNA reads with bowtie2. Were you able to keep both the paired and unpaired reads?

    Comment


    • #3
      Have a look at RiboPicker:



      You can download the tool and rRNA databases. It uses a modified version of bwa-sw for alignment against a rRNA database and splits your (paired) reads into rRNA and non-rRNA.

      Boetsie

      Comment


      • #4
        Hello everyone. The --un-conc option outputs unconcordantly aligned pairs in two separate files, as you mention. The correct option for broken pairs is --un as before. include both flags in your statement


        Code:
        bowtie2 -p 8 -X 430 --un-conc /output/filt_pairs.fq --un /output/filt_single.fq rRNA -1 /input/left.fq -2 /input/right.fq
        will output the filtered pairs in /output/filt_pairs.fq.1 and /output/filt_pairs.fq.2

        and the single reads will be in /output/filt_single.fq

        Hope this helps.
        Cheers

        Comment

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