Announcement

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

  • a trans-chromosomal "proper pair"?

    How could two reads define a "proper pair" when they do not map on the same target? Here are the bam entries I do not understand (from bwa):

    Code:
    HWI-ST314:228:C1NU0ACXX:6:2205:3950:78621       99      chr1    315318847       29      10M1D12M14S     chr2    3874    0       GGATGGGGTGAAGCTGGAGGATAGGCGCCCCATCTG     IJJIJJJJJJJJJJJJJJJJIJJHHHGHFFFFFCCC    XT:A:M  NM:i:5  SM:i:29 AM:i:29 XM:i:4  XO:i:1  XG:i:1  MD:Z:2C2T4^C1G6A3
    HWI-ST314:228:C1NU0ACXX:6:2205:3950:78621       147     chr2    3874    29      36M     chr1    315318847       0       CCATGAGGCACAGGCGGTAGCATTCAGGGCAGTGCC     CCCFFFFFHHHHHGJJJGHIIIJIJJJJJIJIJIIJ    XT:A:U  NM:i:0  SM:i:29 AM:i:29 X0:i:1  X1:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:36
    Flag 99:
    read paired
    read mapped in proper pair
    mate reverse strand
    first in pair

    Flag 147:
    read paired
    read mapped in proper pair
    read reverse strand
    second in pair


    How can they map on different chromosomes (chr1 and chr2) and still qualify as "proper pair"? While most of the "proper pairs" in this file do map on the same target (and in a convergent orientation, with an insert size in the expected range), I do not understand a couple of them...

    Thanks for any comment.

Latest Articles

Collapse

  • seqadmin
    Advanced Methods for the Detection of Infectious Disease
    by seqadmin




    The recent pandemic caused worldwide health, economic, and social disruptions with its reverberations still felt today. A key takeaway from this event is the need for accurate and accessible tools for detecting and tracking infectious diseases. Timely identification is essential for early intervention, managing outbreaks, and preventing their spread. This article reviews several valuable tools employed in the detection and surveillance of infectious diseases.
    ...
    Yesterday, 01:15 PM
  • seqadmin
    Strategies for Investigating the Microbiome
    by seqadmin




    Microbiome research has led to the discovery of important connections to human and environmental health. Sequencing has become a core investigational tool in microbiome research, a subject that we covered during a recent webinar. Our expert speakers shared a number of advancements including improved experimental workflows, research involving transmission dynamics, and invaluable analysis resources. This article recaps their informative presentations, offering insights...
    11-09-2023, 07:02 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:12 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 11-22-2023, 09:29 AM
1 response
51 views
0 likes
Last Post VilliamPast  
Started by seqadmin, 11-22-2023, 08:53 AM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 11-21-2023, 08:24 AM
0 responses
31 views
0 likes
Last Post seqadmin  
Working...
X