Hi,
I downloaded phastcons score of mouse (mm9) through FTP
(hgdownload.cse.ucsc.edu) from
/goldenPath/mm9/phastCons30way/vertebrate. I checked file, chr1.data &
found that first block starts at 3000306, whereas next block starts at
3002512. See below-
fixedStep chrom=chr1 start=3000306 step=1
fixedStep chrom=chr1 start=3002512 step=1
I believe each line on this file represents each position of chromosome,
being step=1. Please clarify if i am wrong.
The difference between beginning of above 2 blocks is 2207, but i found
only 2175 lines for phastcons score. This indicate that phastcons scores
of few bases (about 32) are not given in the file. Does it mean 32
nucleotides before start of next block (i.e. 3002512) do not show
alignment & thus no score. Please clarify.
Another query, If i wish to calculate conservation score of a stretch of
7-8 nucleotides, what should i adopt.
Lastly, if i wish to convert chromosomal coordinates of these files into
positions within the gene, which method or track file of mm9 should i use.
Thank you in advance.
regards,
Bibek
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