Drosophila Bioinformatics- How to tell how many chromosomes from SAM file to get X:A to determine Sex

Question

[Crystal]

I'm trying to determine the Drosophila melanogaster sex using a SAM file upon aligning the sequences with BWA. I understand you need to look at the X chromosome to Autosome ratio (X:A). I didn't perform this paired-end sequencing run on an Illumina HiSeq machine. However I'm assuming I have the following chromosomes: 2, 3, 4 and two X. This gives X:A ratio of 0.66 which is intersex. Is this the correct interpretation, I can't seem to see if theres is indeed more than one X chromosome or if there is only one, from the file. Or is a better way to map X chromosome to a chromosome of similar length as use that as a representative?

Answer 1

[Istvan Albert]

The information that you list above represents the file used to align the data against (the structure of the reference genome). It is not related the alignments in any other way. The same header would be present regardless of what data you aligned against the same reference.

To estimate the copy number look at the coverage of the chromosome X relative to autosomal chromosomes, here is writeup:

https://gaworkshop.readthedocs.io/en/latest/contents/03_sexdet/sexdet.html

also a recent related thread on similar topic

New graduate student in Computational Biology, confused by reads versus copy number!