Clarifying the Meaning of Coordinates, Strand, and Score in BED Files and liftover Results
Chen Lou
Title: Clarifying the Meaning of Coordinates, Strand, and Score in BED Files and liftover Results
① Is this viewpoint correct?
“BED (and Interval) datasets always have coordinates reported in the forward direction, with the strand used as a modifier for the orientation of the region (which can be interpreted as the direction of transcription for BED datasets representing transcripts or portions of transcripts).”
In other words, for example in a BED6 file:
BED format
chrom chromStart chromEnd name score strand
Are chrom, chromStart, and chromEnd always coordinates on the forward strand (regardless of whether the strand column is + or −)?
Is the strand column only indicating something like the transcription direction of the feature (e.g., a transcript name), and does not affect the values of chromStart and chromEnd themselves?
② In addition, I do not quite understand the meaning of the score field. After performing a liftover on a BED6 file, why do all the score values become 1, 2, 3, 4, … in this kind of order?
For example, an original record like:
chr1 135095477 145095477 Pos1 100 +
After liftover, it becomes:
chr3 196625625 196625749 Pos1 1 -
chr3 196625667 196625749 Pos1 2 -
chr3 196625622 196625775 Pos1 3 -
chr3 196625625 196625667 Pos1 4 -
…
Gerardo Perez
Hello,
Thank you for your interest in the Genome Browser and for sending your inquiry.
Yes, in the BED format, the chrom, chromStart, and chromEnd fields define the positions of a BED entry along the reference genome sequence, where the genome reference sequence is displayed in the forward (positive) orientation. The strand column indicates the strand orientation of the BED entry so it can be displayed in either the forward or reverse direction along the reference sequence. The strand column does not affect the chromStart or chromEnd values.
Regarding the score values incrementing (1, 2, 3, 4…) after running LiftOver, this is a bug. The score value should remain the same after LiftOver. We have created an internal ticket to address this issue, but we are not able to provide an estimated timeline for the fix.
Thank you again for bringing this to our attention.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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