fool proof faidx .bed file documentation
darked89 opened this issue · comments
Darek Kedra commented
Hello,
Since probably I was neither the first nor the last bitten by the 1-based faidx command line coordinates and a say region.bed 0-based ones it may make sense to add:
-b BED, --bed BED bed file of regions (zero based)
Hope it helps,
DK
Matt Shirley commented
Thanks for the suggestion. Indeed 0-based vs 1-based start coordinates will be confusing Bioinformaticians for decades to come. I’ll post the coordinate description here for posterity and release a new version with this change.