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, -- Doo Yang Graduate Student University of Ottawa, BMI Department Microbiology & Immunology, Bioinformatics 4208-451 Smyth Rd., Ottawa, ON K1H 8M5 Tel) 613-562-5800 ext. 6932 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
