Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to represent reference and observed alleles in BED files for variants on negative

    Hi Everyone,

    I have a question about the BED detail format described on the UCSC browser webpage. http://genome.ucsc.edu/FAQ/FAQformat#format1

    There is an example there as the following:
    track name=pairedReads description="Clone Paired Reads" useScore=1
    chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
    chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601


    I have a BED file with the similar format as above. I converted it to a BEDdetail format as the following:

    track name=pairedReads description="Clone Paired Reads" useScore=1, type=bedDetail
    chr22 1000 1003 cloneA 960 + 1000 5000 0 2 567,488, 0,3512,ReferenceAllele=C, ObservedAllele=TTT

    chr22 2000 2005 cloneB 900 - 2000 6000 0 2 433,399, 0,3601, ReferenceAllele=CGC, ObservedAllele=AAACT


    I added allele information as well in the free text field of the BED file.

    My question is:

    For the BED record that has the strand information as negative in the above example, is there a BED file format convention to still report the alleles on the positive strand?


    Since there is a strong convention of represent everything in positive strand.
    My guess is that even if a variant on BED file has strand field as "negative", I should still report the allele information from the positive strand.

    I would really appreciate anyone's feedback on this. I would like to do what the convention is in BED files, however, so far I didn't see any posts about this.

    Thank you,
    Laura

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
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
70 views
0 likes
Last Post seqadmin  
Working...
X