ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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The function convertEnsemblToNames.py get error! #129
Hi! : )
When I check the script, I found that error caused by this part [line 23-26]:
loads a map with the ensembl ids -> gene name
gene_map = dict()
for line in gff_lines(annotation):
gene_map[line["gene_id"]] = line["gene_name"]
I think this is because some genes from ensemble gtf file have not gene_name, this is a small bug.
And another question is that, some gene ids refer to one gene name, it seems the script only transfer one of the gene id to the gene name, I wonder if it is acceptable.
Hi! : ) When I check the script, I found that error caused by this part [line 23-26]:
loads a map with the ensembl ids -> gene name
I think this is because some genes from ensemble gtf file have not gene_name, this is a small bug. And another question is that, some gene ids refer to one gene name, it seems the script only transfer one of the gene id to the gene name, I wonder if it is acceptable.