gff3 file error when running majiq input

[Maoting Chen]

Dear Majiq team,

I am running AS analysis on my data using MAJIQ v3 and previously I have used v2 for the same dataset. 

With the same gff3 file, I got an error which didn't show up when I used v2:

I got the gff3 file from ensembl directly and it's a old release. But i don't want to change to newer release because i used the gtf file of the same release for mapping. Is there any way I can bypass such errors?

Thank you,

Maoting

[San Jewell]

Hi Maoting, 

I have seen this error before, and in the file I was looking at there were indeed one or two definitions which were actually zero-length, seemingly a mistake when the annotation was created. It may be a similar case here. I would check those coordinates that are indicated and remove that specific transcript from the annotation. If it's just one or two transcripts it should not have significant affect on your analysis (and v2 was just silently ignoring it anyway) 

Let me know if it makes sense. 

Thanks, 

-San

[Maoting Chen]

Hi San,

Thank you for your reply.

As I proceeded with my analysis, the tsv file from majiq psi doesn't contain the column for LSVs. As you can see from the screenshot of the tsv output, every entry is a junction. Is it something expected? How to get LSV-based output like v2?

Thank you,

Maoting

[Maoting Chen]

And also, it's surprising to see that the ref_exon_start for some junctions is -1 in the below screenshot. Is there anything wrong with the build step?

Thank you,

Maoting