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
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?)
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
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version 2.3.6
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.