kbchoi-jax
commented
8 years ago I guess you got around it already. Could you share what the issue was?
Closed lassancejm closed 8 years ago
kbchoi-jax
commented
8 years ago I guess you got around it already. Could you share what the issue was?
Hi,
I am willing to run Emase with F1 hybrid data and am running into an issue during the reference preparation.
Basically, everything seems to be running fine (i.e. no error message produced), but the step "Recording mapping of gene id to transcript id's..." results into an empty emase.gene2transcripts.tsv file.
Here is an example from the GTF, where gene1 encodes clearly several transcripts.
NW_006501037.1 . exon 6936 7096 0 - . gene_id "gene1"; transcript_id "mRNA1"; NW_006501037.1 . CDS 6936 7096 0 - 2 gene_id "gene1"; transcript_id "mRNA1"; NW_006501037.1 . exon 6936 7096 0 - . gene_id "gene1"; transcript_id "mRNA3"; NW_006501037.1 . CDS 6936 7096 0 - 2 gene_id "gene1"; transcript_id "mRNA3"; NW_006501037.1 . exon 6936 7096 0 - . gene_id "gene1"; transcript_id "mRNA4"; NW_006501037.1 . CDS 6936 7096 0 - 2 gene_id "gene1"; transcript_id "mRNA4"; NW_006501037.1 . exon 64350 64488 0 - . gene_id "gene1"; transcript_id "mRNA1"; NW_006501037.1 . CDS 64350 64488 0 - 0 gene_id "gene1"; transcript_id "mRNA1"; NW_006501037.1 . exon 64350 64488 0 - . gene_id "gene1"; transcript_id "mRNA3"; NW_006501037.1 . CDS 64350 64488 0 - 0 gene_id "gene1"; transcript_id "mRNA3";
Do you have an idea of what may be going on here? Can I generate this file in any other way?
Thanks
JM