Question: Where Is The Tss Of A Gene Located In A Bed File?
1
gravatar for KCC
8.4 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

I have been trying to figure out which end of a gene specified in a BED file is the transcription start position. I believe that for the forward (+) strand the transcription start site(TSS) should be in the BED file's start column while for the gene on the reverse strand (-), the TSS would be in the 'end' column of the bed. Is that true? So for example,

chr1 100 5000 Gene1 0 +

chr1 30000 49023 Gene2 0 -

Suppose the information above is from a bed file: chromosome, start, end, feature name, score, strand. Assuming either the start or end coordinate specifies the TSS, is it correct to conclude that 100 is the TSS for Gene1 and 49022 is the TSS for Gene2? (I say 49022 because the last coordinate of a BED feature is not included in the feature.)

bed • 3.2k views
ADD COMMENTlink modified 8.4 years ago by seidel7.1k • written 8.4 years ago by KCC4.0k
1

that is correct

ADD REPLYlink written 8.4 years ago by Gjain5.5k
2
gravatar for seidel
8.4 years ago by
seidel7.1k
United States
seidel7.1k wrote:

BED files don't know anything about genes. They simply specify features (segments) on a genome. However they do so in a way such that start is lower than end, and strand can be specified. So if you know your features are genes, the your interpretation is correct.

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by seidel7.1k
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