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SchulzLab / Aeron

Alignment, quantification and fusion prediction from long RNA reads
MIT License
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GraphBuilder outputs empty file #27

Open majorkazer opened 3 years ago

majorkazer commented 3 years ago

Hello,

I am trying to get started using Aeron on some long read data generated from murine macrophages. I am attempting to build the graph using the following command, but get the output below and the gta file is empty.

$ python GraphBuilder.py -e mm10.fa -g ref-transcripts.gtf -o mm10.gta
Reading Sequences
Done reading sequences
Reading and processing gtf
Done reading gtf
Collecting all the genes
Building graph for:
Warning: No sequence information added
Warning: No connection information added
readmanchiu commented 3 years ago

Hi,

I got the same problem with an empty gfa produced. Seems like when it iterate through the transcript all the steps were able to return non-empty variables except the last step getNodeConnections()

yeroslaviz commented 2 years ago

Did anyone found a solution for this problem? I have the same empty file. I'm working with C. elegans. Can it has anything to do with the genome one works with?

thanks