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Question: package for sex determination using sam/bam files
1
gravatar for Pau Marc Muñoz Torres
2.1 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

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Pau Marc Muñoz Torres20
1
gravatar for Martin Morgan
2.1 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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?)

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Martin Morgan ♦♦ 20k
0
gravatar for Pau Marc Muñoz Torres
2.1 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)

 

http://seqanswers.com/forums/showthread.php?t=63360

 

ADD COMMENTlink written 2.1 years ago by Pau Marc Muñoz Torres20

You should be safe if you're using an aligner with a concept of "unique" alignment. Reads originating from any homologous region in both chromosomes X and Y should not be mapped to either. Thus, you should be able interpret the counts for each chromosome directly. Another approach, depending on the type of data you have, is to look at the expression of the Xist gene; high expression should only be present in females where X-inactivation is present.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Aaron Lun17k
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