problems for gff_make_annotation.py

[pengchy]

Hi Yarden,

This is a great package.

I have used gff_make_annotation.py to prepare events gff3 files for running MISO. However, I have several questions about gene_id of the RI.gff3 file:

1. the separator between the start and end position in RI are hyphens "-", while others are colons ":".
2. The start and end position of the events on the negative strand not always in the same order. Such as the following case:
   scaffold10083:71811-70750:-@scaffold10083:70693-70386:- # in which the left number of the hyphen is bigger than the right.
   scaffold7844:217202-218197:+@scaffold7844:218210-218580:+ # in which the left number of the hyphen is smaller than the right, which is same to all other events (MXE and SE)

Could this situation influence the MISO results? I want to utilize the exon information just from the gene_id, so I found the problem. The running of MISO using this GFF3 has not report any problems.

Best,
Pengcheng Yang