Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie2: mapping qualities in paired end mode different with the single mode

    Hello,

    I am using Bowtie2 for paired-end alignments and I noticed a strange behavior: the mapping quality scores are not the same if the alignment is done in paired end mode or with the two mates mapped independently. The differences come with ambiguous sequences.For example :

    - in paired-end mode :

    HISEQ:3291TN8ACXX:6:2306:8678:87560 65 ecoliK12 19558 44 7S84M = 3581916 0 CGACAAACCGGCGGGACAGCGAATCTGCAATACGGATTATTCTGCGCTTTTTAGTCCAGCGGTGCGTTAATCGGCAGCTCCCCCAGAGATA FFFBFEGID8?FFB'5?D;=6>B@BBDBBABB:?@898A9BD>9>0&75?A3?B4>@B99)5908<5?AA<<<-5?>@########### AS:i:156 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:7T70A2T2 YT:Z:UP

    HISEQ:3291TN8ACXX:6:2306:8678:87560 129 ecoliK12 3581916 44 90M1S = 19558 0 CACGTATTCGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATAAGGATGATGGATGGCC F><<+A?C?+;E;CB?<11?D*:?DB:067@';/;''3;99?>@::>>A55<CC>::4:<1>4>C@######################### AS:i:172 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:75T6C7 YT:Z:UP


    - with alignment of the two mates one after the other:

    bowtie2-2.1.0/bowtie2 -x /data/genomes_bact/ecoliK12 -p6 --sam-no-hd --sam-no-sq --quiet --local--very-sensitive-local -c CGACAAACCGGCGGGACAGCGAATCTGCAATACGGATTATTCTGCGCTTTTTAGTCCAGCGGTGCGTTAATCGGCAGCTCCCCCAGAGATA

    0 0 ecoliK12 19558 42 7S78M6S * 0 0 CGACAAACCGGCGGGACAGCGAATCTGCAATACGGATTATTCTGCGCTTTTTAGTCCAGCGGTGCGTTAATCGGCAGCTCCCCCAGAGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:148 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7T70 YT:Z:UU

    > bowtie2-2.1.0/bowtie2 -x /data/genomes_bact/ecoliK12 -p6 --sam-no-hd --sam-no-sq --quiet --local --very-sensitive-local -c CACGTATTCGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATAAGGATGATGGATGGCC

    0 0 ecoliK12 3581916 1 90M1S * 0 0 CACGTATTCGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATAAGGATGATGGATGGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:164 XS:i:164 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:75T6C7 YT:Z:UU

    It is quite disconcerting for me since I though the mapping quality was calculated independently of the relation with the mate. I know in the paired end mode it will try to find near mates but if it cannot, it will normally give an independant position with the true Mapping quality score.What do you think?

  • #2
    With bowtie2, mates will always have the same quality, since you're mapping them as a unit. Since the mapping position of one mate is dependent on the mapping position of the other, this generally makes sense. Also, bowtie2's MAPQs aren't those defined in the SAM spec., so you'll see other weird behavior there if you look really closely.

    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
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    66 views
    0 likes
    Last Post seqadmin  
    Working...
    X