#4 If target and query on different strand might cause incorrect coordinate conversion

[Limei Chiang]

Hi,
I used CrossMap v0.2.7 to perform a liftover on a gff3 file, but the coordinates of some featuresin the output file are weird.
Here is the example:
Chain file

chain 7258 AYNB01128118.1 7258 + 0 7258 NW_019289416.1 541776 - 293460 300718 822
7258

input feature:

AYNB01128118.1  OGSv1.0 gene    1639    6761    .       +       .    ID=LDEC024741

output feature:

NW_019289416.1  OGSv1.0 gene    241556  246678  .       -       .    ID=LDEC024741

The start and end coordinates of the output feature are not within the region (293460-300718) in the alignment line in chain file. Besides, If you convert these features into a Fasta file, you can find that these two gene sequence is totally different.

Thanks,
Limei