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 -
…