Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X