Usual chromosome naming conventions things etc. (but I suspect not so much issue as use same ref for Stringtie and filtering)
strings/naming conventions for attributes e.g. 'gene_type' & their associated protein-coding/lncRNA flags etc. (I think it's gene_biotype...)
And I'm sure I can think of other things down the line...
I suspect I'll need to add some options to config and to CLI of filter_by_tx_chain.py... Reckon set defaults at the bottom e.g.
# gencode/ensembl
gtf_style: gencode
gencode:
gene_type_col: "gene_type"
pc_lnc_flags: ["protein_coding", "lncRNA"]
ensembl:
gene_type_col: "gene_biotype"
# and same for pc_lnc_flags but not sure what they are...
closed with b970bb05 - from manual checks the only difference is the gene_type column. Extra CL option to specify whether reference source is gencode/ensembl
And I'm sure I can think of other things down the line...
I suspect I'll need to add some options to config and to CLI of
filter_by_tx_chain.py
... Reckon set defaults at the bottom e.g.