i need whole genome pairwise alignment between human and gorilla and chimp. I found the paiwise alignment file in UCSC genome browser http://hgdownload.soe.ucsc.edu/downloads.html
but i dont understand the structure of files there , they are some numbers without any nucleotide or usual alignment structure there, structure like this:
in the net file: fill 1395 20015 chrUn + 1855136 20062 id 2914 scor 1590070 ali 19664 qDup 19767 type top tN 0 qN 176 tR 14871 qR 14596 tTrf 287 qTrf 356 gap 3541 1 chrUn + 1855482 0 tN 0 qN 0 tR 1 qR 0 tTrf 0 qTrf 0
in the chain file:
chain 17470905528 chr1 249250621 + 87771 248804627 chr1 228333871 + 77636 228159347 1
15 1 0
6 1 0
what is the difference between net and chain files? i appreciate if anybody could help me how i can analyze these files?
•
written
by
masih.mahmoudi •
1 answer
You should read description of the files on the download page. This would point you to the explanation of net and chain files.
Log in to answer this question.
Hi, I liked the descriptions here - http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto http://genomewiki.ucsc.edu/index.php/Chains_Nets