Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • from gene coverage to sex determination

    Hello everybody

    I am interested in determining sex from my nextseq runs. I read somewhere that a possibility is to calculate gene coverage for X and Y genes and then do sex determination

    if cov(x)> cov(y) -> XX
    if cov(x)~=cov(y) -> XY

    to determine X coverage in Linux I am using samtools

    samtools view <file.bam> RNAME 'chr[XY]'|wc -l

    and the data I'm getting looks like

    paumarc@bioinf[refSamples] samtools view wtsorted.bam RNAME 'chrY'|wc -l [ 4:39]
    [main_samview] region "RNAME" specifies an unknown reference name. Continue anyway.
    93504
    paumarc@bioinf[refSamples] samtools view wtsorted.bam RNAME 'chrX'|wc -l [ 4:39]
    [main_samview] region "RNAME" specifies an unknown reference name. Continue anyway.
    1020263

    The question is: Can I determinate sex only with this or i should do some kind of correction? it is normal to have more reads on chrx as long as it is bigger)

    thanks

    pau
    Last edited by paumarc; 10-09-2015, 06:44 AM.

  • #2
    You'll definitely need to correct for the difference in size (Y is much smaller than X), but they may have differences in mappability as well. I would encourage you to look at a few samples for which you know the gender and that'll give you some decent numbers to start with.

    BTW, "samtools view -c foo.bam chrX" will be faster than piping to "wc -l".

    Comment


    • #3
      With samtools idxstats you'll get the result even faster plus the length of the chromosomes.

      Since you may get mapping artefacts from intron regions, you can use a bed-file of known (chrY / chrX) - genes to limit your look-up:
      Code:
      samtools view -c -L chrX-genes.bed foo.bam 
      samtools view -c -L chrY-genes.bed foo.bam
      The result should be corrected, as Devon posted.

      BTW.: in your command you use the keyword RNAME; this is not necassary.

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