Genes with one transcript are ignored without warning and are not included in the pairwise distance file when running TranD in pairwise mode. This leads to these genes being excluded from any analysis using the pairwise distance file (e.g. ERG generation).
There is a current workaround: use the "find_genes_with_one_transcript.py" utility on the GTF(s) being input into TranD to generate a list of genes with only one transcript and keep track of them.
Genes with one transcript are ignored without warning and are not included in the pairwise distance file when running TranD in pairwise mode. This leads to these genes being excluded from any analysis using the pairwise distance file (e.g. ERG generation).
There is a current workaround: use the "find_genes_with_one_transcript.py" utility on the GTF(s) being input into TranD to generate a list of genes with only one transcript and keep track of them.