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Question: package for sex determination using sam/bam files
1
3.0 years ago by
Barcelona
Pau Marc Muñoz Torres20 wrote:

Hello everybody

I would like to know if exists some package in bioconductor that could be used for determining the sex in samples coming from sequenciation files in bam or sam format? I saw massiR can be used to determine sex in samples of microarray analysis but not for sam files

exists some easy technique to do this determination?

thanks

modified 3.0 years ago • written 3.0 years ago by Pau Marc Muñoz Torres20
1
3.0 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Is it as easy as counting the number of reads aligning to the Y chromosome?

library(Rsamtools)
bfl = BamFileList(dir(pattern="bam\$"))
which = as(seqinfo(bfl)["chrY"], "GRanges")
param = ScanBamParam(which=which)
countBam(bfl, param=param)

(I guess this could be formalized, but would it be necessary?)

0
3.0 years ago by
Barcelona
Pau Marc Muñoz Torres20 wrote:

it should be, but I am not sure if chromosome X and Y share some regions or not.

http://onlinelibrary.wiley.com/doi/10.1038/npg.els.0005793/abstract

in that case how can I be sure that the reads  I have in X are not homologous at Y as well?

I have got this answer at seqanswers, but I am not sure (I am new working with nextseq)