Closed kubu4 closed 3 months ago
Oh my, you are correct. Looks like the coordinates in the headers of the mir.fasta file are incorrect. I bet it is because, internally, I use bed coordinates which are zero-based half open, but forgot to convert to one-based fully closed which is what I mean to put in the output. Should be a simple patch...
Yes, internally ShortStack using bedtools getfasta
with a temporary BED file to write the FASTA of microRNAs, microRNA-stars, and precursors. The headers are auto-generated by bedtools getfasta
, which used BED-style (zero-based, half-open) genomic coordinates instead of the one-based, fully closed coordinates that one expects for tools like samtools
. So the coordinates are correct, but the coordinate system diverges from what I would consider the more "normal" one-based fully closed coordinate system.
As of commit bab44af the coordinates in the headers of file mir.fasta are now in one-based, fully-closed coordinate system.
This will be included in the next release (not sure when that will be).
Thanks for pointing this out!
The
Results.gff3
starting coordinates are1
greater than those listed in the FastA description lines.Here's an example that I'm seeing (this holds true for all the sequnces in both files, though):
The
Results.gff3
lists the starting position as:12757147
The
mir.fasta
lists the starting position as:12757146
If using the gff3 start/stop positions, then the expected length of the sequence would be 22 bases. Examine the length of the sequence in the corresponding FastA entry:
We see that 22 bases is indeed the length, so it appears that the FastA description line is incorrect for some reason.