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Old 02-17-2012, 12:47 PM   #1
LauraSmith
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Location: SAN FRANCISCO

Join Date: Dec 2011
Posts: 4
Post How to represent reference and observed alleles in BED files for variants on negative

Hi Everyone,

I have a question about the BED detail format described on the UCSC browser webpage. http://genome.ucsc.edu/FAQ/FAQformat#format1

There is an example there as the following:
track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601


I have a BED file with the similar format as above. I converted it to a BEDdetail format as the following:

track name=pairedReads description="Clone Paired Reads" useScore=1, type=bedDetail
chr22 1000 1003 cloneA 960 + 1000 5000 0 2 567,488, 0,3512,ReferenceAllele=C, ObservedAllele=TTT

chr22 2000 2005 cloneB 900 - 2000 6000 0 2 433,399, 0,3601, ReferenceAllele=CGC, ObservedAllele=AAACT


I added allele information as well in the free text field of the BED file.

My question is:

For the BED record that has the strand information as negative in the above example, is there a BED file format convention to still report the alleles on the positive strand?


Since there is a strong convention of represent everything in positive strand.
My guess is that even if a variant on BED file has strand field as "negative", I should still report the allele information from the positive strand.

I would really appreciate anyone's feedback on this. I would like to do what the convention is in BED files, however, so far I didn't see any posts about this.

Thank you,
Laura
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