Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • samtools flagstat reports an odd number of reads "with itself and mate mapped"

    How can "samtools flagstat" report an odd number of reads "with itself and mate mapped"? I don't get that...

    samtools flagstat reads.bam

    Code:
    161533046 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    137350248 + 0 mapped (85.03%:-nan%)
    161533046 + 0 paired in sequencing
    80766523 + 0 read1
    80766523 + 0 read2
    106075436 + 0 properly paired (65.67%:-nan%)
    124869771 + 0 with itself and mate mapped
    12480477 + 0 singletons (7.73%:-nan%)
    8181512 + 0 with mate mapped to a different chr
    4410235 + 0 with mate mapped to a different chr (mapQ>=5)
    Any idea?
    Reads come from a mate pair protocol, sequenced on HiSeq, aligned by bwa.
    Thanks!

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, 03-27-2024, 06:37 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X