I downloaded a list of
refseq genes from the
table browser -
bed format. From the bed format description given by UCSC, thickStart and thickEnd means:
thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays). thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
This has gotten me a bit confused. To explain my confusion look at the following sample bed file from UCSC.
chrI 7741935 8394405 NR_070240 0 + 8394405 8394405 0 8 18,12,13,9,11,11,8,18, 0,209004,270977,272247,461655,519425,544710,652452, chrI 8378298 8390022 NM_001129046 0 - 8378298 8390022 0 8 123,103,110,116,65,69,124,113, 0,832,1401,2025,9723,9836,10481,11611,
So, what do columns 2 (start) and 3 (end) mean? And how are they different from columns 7 (thickStart) and 8 (thickEnd)? They seem be different in most of the cases! I thought col 2 and 3 mean meant the starting and ending positions of the genes. But the definition of
thickEnd has gotten me confused.
Here is the link to bed file description given by UCSC.