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  • 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

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