Human chrY analysis

Question

[cpfiel]

Hi,

I have downloaded the sequence for CHR_Y from ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/ because I want to analyze it and to understand it.

In Linux when I run the command:

cat ref_chrY.gbk | grep -n "ORIGIN"

I get all the lines with the word ORIGIN. I don't understand this because I thought I would download one sequence of the Y human chromosome, but it seems that I have 16 sequences there. I have found other fasta file in http://hgdownload.cse.ucsc.edu/downloads.html and this is only one sequence.

Best, Carlos

[WouterDeCoster]

hi cpfiel,

Your question will not get more attention if you put the title in capital letters. There is no need to "shout". I have adapted your post.

Cheers,
Wouter

[cpfiel]

Oh, I didn't know it. Thank you for the correction.

Answer 1

[tdmurphy]

The files in the CHR_* directories are for the scaffolds assigned to each chromosome, including the set of 13 scaffolds used to make the GRCh38 Y chromosome plus 3 extra unlocalized scaffolds assigned to chrY but not yet incorporated into the chromosome. If you want the assembled chrY sequence, try one of these files: ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/Assembled_chromosomes/gbs/hs_ref_GRCh38.p7_chrY.gbs.gz ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens//Assembled_chromosomes/seq/hs_ref_GRCh38.p7_chrY.fa.gz

If you want to understand the set of sequences used to assemble the chromosome, try the AGP file instead: ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens//Assembled_chromosomes/agp/hs_ref_GRCh38.p7_chrY.agp.gz

[cpfiel]

Hi tdmurphy,

Thank you very much :). That is very helpful.

Best