Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie giving opposite results

    Hi all,

    I am using the bowtie program to run alignments on a set of mate pair data (2 fastq files) and have run into a problem. What I have found is that if I run bowtie with the regular fastq files 'as is' with the --rf (MP orientation) option, then the results I get are "backwards", in the sense that reads with large insert sizes of 1000+ are being given bitFlags that indicate paired end orientation, and reads with smaller insert sizes of around 180 are being given mate pair orientation when they are clearly paired end. I also ran bowtie with the reverse complemented fastq files (accomplished this using a python script that reverse complemented the bases, and reversed the quality scores), and this time, bowtie2 gave bitFlags that made sense with the data, i.e. expected mate pair reads were being given bitFlag definitions of mate pair orientation. I am not sure if this is expected, and I should be giving bowtie the reverse complements of these fastq files, or if I have made a mistake in another option? I did specify '--rf' to indicate the data was MP, and gave -I and -X options.

    /home/rcorbett/aligners/bowtie2/bowtie2-2.0.0-beta7/bowtie2 -p 8 --rf -I 2000 -X 2500 -x /home/rcorbett/aligners/bowtie2/bowtie2-2.0.0-beta7/hg19a -1 /projects/rcook/3_prj/bwa/30NE8AAXX_3_1_export_f1b6.fastq -2 /projects/rcook/3_prj/bwa/30NE8AAXX_3_2_export_f1b6.fastq -S /projects/rcook/3_prj/bowtie.align.output.rf.min2000.max2500.sam
    Thanks to anyone who takes the time to read and respond to this post!

    Riley
    Last edited by rcook34; 11-08-2012, 10:43 AM.

  • #2
    Solution

    I found out it was a bad set of data. Used bowtie2 to map a completely different set of mate pair data and it worked as it should. Seriously though, a few weeks and 132 views and no one responds? awesome...

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    23 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    18 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Working...
    X