Which Files At Ucsc Contain The Phastcon Scores

Question

[neebasebastian]

Hi,

I am planning to download the phastcon scores from

ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/placentalMammals/

But For some chromosomes I saw multiple files.

chr17.phastCons46way.placental.wigFix.gz
chr17_ctg5_hap1.phastCons46way.placental.wigFix.gz
chr17_gl000203_random.phastCons46way.placental.wigFix.gz
chr17_gl000204_random.phastCons46way.placental.wigFix.gz
chr17_gl000205_random.phastCons46way.placental.wigFix.gz
chr17_gl000206_random.phastCons46way.placental.wigFix.gz
`

Can you please explain. Is this all files are necessary or only take the first one (chr17.phastCons46way.placental.wigFix.gz)?

Answer 1

[biorepine]

Just use chr17.* and ignore the random chromosomes .

Answer 2

[Ian]

Also ignore the chr17ctg5hap1 (an alternative haplotype for part of chr17).

BTW "random" are unassembled contigs thought to belong to chr17.

Some more explanation can be found at the UCSC FAQ.