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
          Quality Control Essentials for Next-Generation Sequencing Workflows
          by seqadmin




          Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

          Nucleic Acid Quality Control
          Preparing for NGS starts with isolating the...
          Yesterday, 01:58 PM
        • seqadmin
          An Introduction to the Technologies Transforming Precision Medicine
          by seqadmin


          In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
          01-27-2025, 07:46 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-07-2025, 09:30 AM
        0 responses
        20 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-05-2025, 10:34 AM
        0 responses
        37 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-03-2025, 09:07 AM
        0 responses
        37 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 01-31-2025, 08:31 AM
        0 responses
        42 views
        0 likes
        Last Post seqadmin  
        Working...
        X