YFP reporter lacking exon_number

Hello,

I seem to have a problem with my genes.gtf input file; ther reporter_YFP is lacking the exon_number feature. Any ideas on how to circumvent the issue?

Below is a snippet of my command, and traceback/error.

Also note, I had to switch to run, instead of run10x, because my cellranger output file was likely an older version, which caused problems.

Thanks.

sudo velocyto run -m mm10_rmsk.gtf e12_outs/possorted_genome_bam.bam genes.gtf

# ...

# 2018-11-01 21:55:25,892 - DEBUG - Parsing Chromosome reporter_YFP strand + [line 1409510]
# Traceback (most recent call last):
#   File "/Users/cahanlab/anaconda3/envs/veloEnv/lib/python3.6/site-packages/velocyto/counter.py", line 519, in read_transcriptmodels
#     exonno = regex_exonno.search(tags).group(1)
# AttributeError: 'NoneType' object has no attribute 'group'
# 
# During handling of the above exception, another exception occurred:

# ... 

# File "/Users/cahanlab/anaconda3/envs/veloEnv/lib/python3.6/site-packages/velocyto/counter.py", line 522, in read_transcriptmodels
# raise IOError("The genome annotation .gtf file provided does not contain exon_number. `exon_number` is described as a mandatory field by GENCODE gtf file specification and we rely on it for easier processing")

[jayypaul]

did you manage to circumvent the issue? facing the same

Yeah, had to go into the gtf file & manually add in “exon_number” annotation for the extra genes that we had added into the file at the end.

[ShobiStassen]

@jayypaul @cstrlln @Rui-Jing Hi, I’m facing exactly the same problem when running velocyto (.gtf file provided does not contain exon_number.) Do you mind sharing how you managed to circumvent this issue? thanks !