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Question: DNA intervals start stop
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gravatar for laura
3.7 years ago by
laura • 0
laura • 0 wrote:

I just ran extract genomic DNA using an interval file with start and stop calculated from SNP positions as plus and minus 200. This returned 400 bases of sequence; I was expecting 401. Does the sequence start at START, or at START+1?

Thanks

Laura
galaxy • 879 views
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modified 3.7 years ago by Hotz, Hans-Rudolf • 1.8k • written 3.7 years ago by laura • 0
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3.7 years ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi Laura

 

As far as I know, Galaxy's interval file follow the same rules as BED files, i.e. zerobased, end exclusive.

see: http://genome.ucsc.edu/FAQ/FAQformat.html#format1

 

Hans-Rudolf
ADD COMMENT • link written 3.7 years ago by Hotz, Hans-Rudolf • 1.8k

That appears to have been my situation. Thanks for the explanation.

Laura Georgi

American Chestnut Foundation Meadowview Research Farms 29010 Hawthorne Dr Meadowview, VA 24361 tel 276-944-4631 fax 276-944-0934 laura@acf.org

ADD REPLY • link written 3.7 years ago by laura • 0

Hi Laura, If Hans-Rudolf's answer helped you out, please mark it as "accepted" by hovering over the left side of the post and clicking on the checkmark. This helps other to find good solutions. Thank you!! Jen, Galaxy team

ADD REPLY • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

zero based meaning the first base is numbered 0 (not 1), and exclusive meaning that the "stop" base is not included.

ADD REPLY • link written 3.7 years ago by laura • 0
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