Convert
Format to format, without breaking it
Most conversion bugs are silent: an off-by-one coordinate, a dropped strand, a chromosome named two ways. Every page here shows the command and the check that proves it worked.
From GTF
- How to Convert GTF to BED (and Keep Your Coordinates Right)
gtf2bed subtracts one from the start coordinate for you; a naive awk one-liner won't, and that gap costs you a silent off-by-one bug three steps downstream.
From h5ad (AnnData)
- How to Convert h5ad to Seurat object (Without Losing Your Metadata)
anndataR and capseuratconverter handle the transpose and slot mapping for you; deciding which layer actually becomes your counts slot is still on you.