HI,
I am not familiar working with genome annotation data so I have
questions about the output files of CpG island and Refgene from UCSC
browser.
First I have download a table with all the CpG island annotation. The
file have 4 columns 1:chrom name : 2nd and 3rd are start and end
position and the fourth one is the number or name give to each CpG
island. I notice there are different positions with the same number in
the fourth column. Why this happened? Sometimes could be due to the
length of the CpG island (range 201-3000pb) but another times these
position are more than 10kb distant.
The second question is in both cases with CpG island file and Refgene I
got all the features from chromosome 1 until chromosome 22 but later in
the table appear another annotation that I don't really understand.
chr6_dbb_hap3
.
.
ChrUN_...
chr17_ctg5_hap1
...
chr1_gl000191_random
What they are? Should I used them?
Thanks a lot in advance for your help.
María Jesús
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