RUN MAJIQ for simulated/synthetic data

[Onkar Mulay]

Hi,

I want to run MAJIQ for synthetic data, but the gff3 file is creating issue.

Multiple errors like this:

• WARNING - Error, incorrect gff. exon doesn't have valid mRNA b'R2_60_1'
• Transcript doesn't contain one of the ID or parent attributesinformation values: ID
• SRR4011971: 0 LSVs

And I'm not able to execute perl script for gtf to gff3. We hav synthetic gtf, how to convert to gff3?

Regards,

Onkar

[Paul Jewell]

Hello Onkar,

What kind of errors are you getting using the gtf to gff3 script? It should still work. Majiq expects some of the optional last-column field names in the gff3 to be valid, and it looks like in this case the "ID" attribute is missing. Do you think you could forward us the first 100 lines or so of the annotation you are generating so that we can try to debug is here? I'm sure it's something very simple. (and as a bonus, we may be able to update that old script to better handle the cases you are seeing -- it's many years old and even though GTF is a relatively stable standard, it may be the case that there is just some new format that you have downloaded which we don't correctly account for. )

Thanks.

[Onkar Mulay]

sorry for late reply, but I have dropped that plan because gff3 looks quite a lot different