Hello, Doo,
> Does the option count bp including the base specified in the BED file?
I believe you are asking if the BED file contents are included in
the sequences retrieved? If so, then yes. The option says: "Add...."
I'm going to assume you are using the lates Drosophila assembly (dm3)
because you name your track "Dmel..." E.g., If you use the DNA link
in the bluebar at the top of the Browser, and put in only
chrX:23077-23077 for the Position and no padding, you get back A.
If you pad with 1 bp on each side, you get TAC.
For your second question, I'm afraid I'm not understanding what
difficulty you are having. When I put in chrX:23077-23077 and
add 1 bp at the 5' and zero 3', I get two bases: TA. Could you
elaborate?
best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 1/9/2012 10:00 AM, Doo Yang wrote:
> Hi,
>
> I was trying to extract sequences after uploading a BED file.
> I found that the returned sequence and the coordinates were different from
> what I expected.
>
> 1. Add [ ] extra bases upstream (5') and [ ] extra downstream (3')
> I tried to extract 499 bp sequence from upstream (starting from -1) and 100
> bp sequence from downstream, total 600 bp long sequences.
> Then I had to put 500 and 100 as the input for the options to get 600 bp
> long sequences.
> Does the option count bp including the base specified in the BED file?
>
> 2. After extracting the sequence I found the coordinate for + and - had 1
> bp different from what I expected.
> Here is a sample data I used for testing.
>
> This is the BED file with the first two entries.
>
> track name="DmelProm" description="testing UCSC"
> chrX 23076 23076 promoter 0 -
> chrX 23878 23878 promoter 0 +
>
> This is the two results with different extra bases. The original base given
> in the BED input was supposed
> to be included in the 5' segment according to my expectation.
> But the result showed that the given coordinate seemed to be included in
> the "left" segment not upstream nor downstream.
> I'm sort of confused and tried to search for the answer. It doesn't seem to
> result from 0-base problem.
> Would you explain the result for me?
>
> Extra 1 bp at 5' and 0 bp at 3'
>> dm3_ct_DmelProm_7166_promoter range=chrX:23077-23077 5'pad=1 3'pad=0
> strand=- repeatMasking=lower
> T
>> dm3_ct_DmelProm_7166_promoter range=chrX:23878-23878 5'pad=1 3'pad=0
> strand=+ repeatMasking=lower
> T
>
> Extra 0 bp at 5' and 1 bp at 3'
>> dm3_ct_DmelProm_7166_promoter range=chrX:23076-23076 5'pad=0 3'pad=1
> strand=- repeatMasking=lower
> A
>> dm3_ct_DmelProm_7166_promoter range=chrX:23879-23879 5'pad=0 3'pad=1
> strand=+ repeatMasking=lower
> G
>
> Thanks,
>
>
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