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SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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_corrected.gtf file without transcript line #64

Open yemao701 opened 4 years ago

yemao701 commented 4 years ago

I'm running SQANTI_qc2.py (version 7.3.2, the version of cDNA_Cupcake is 11.0.0, python 3.7.4)，with this Parameters:

20200410150536

All the steps were OK until I got this message: error

I check my reference GFF file but it is OK： reference gff

So I check *_corrected.gtf and found that the file has no transcript line. I don't think it's normal: QQ截图20200410141721 Did I do something wrong?

BTW: This is the file that generated by SQANTI2 before error: file

Magdoll commented 4 years ago

@yemao701 ,

Not sure if you fixed it yet, but yeah, something is weird if the input fasta after it got turned into GTF. It's supposed to have one line of "transcript" followed by records for "exons".

-Liz

AminMahpour commented 4 years ago

I can replicate this issue as well. Maybe there is a problem with the GTF handling library?

EDIT: I have narrowed down the issue to the "gffread" command where it cannot create the "transcript" lines.

Magdoll commented 4 years ago

hi @AminMahpour , It may be the gffread version you have? this is my version

$ gffread --version
0.11.4
AminMahpour commented 4 years ago

I’m using the Anaconda-based one, which is 0.11.7. GFFREAD does not seem to have a valid —version argument.

Amin