For upstream_fasta, downstream_fasta ref_fasta running --help will pring the option and explanation on the following line unlike the others. Requesting all to be uniform.
--chrom CHROM Chromosome name (String)
--in_fasta IN_FASTA Path(s) to new sequence(s) to be inserted into reference genome in fasta format
--in_gff IN_GFF Path(s) to GFF file(s) describing new fasta sequence(s) to be inserted
--upstream_fasta UPSTREAM_FASTA
Path(s) to Fasta file(s) with upstream sequence. Either position, or upstream AND downstream
sequence must be provided.
--downstream_fasta DOWNSTREAM_FASTA
Path(s) to Fasta file(s) with downstream sequence. Either position, or upstream AND downstream
sequence must be provided.
--position POSITION Comma-separated positions at which to insert new sequence. Note: Position is 0-based, no space
between each comma. Either position, or upstream AND downstream sequence must be provided.
--ref_fasta REF_FASTA
Path to reference fasta file
--ref_gff REF_GFF Path to reference gff file
For
upstream_fasta,downstream_fastaref_fastarunning --help will pring the option and explanation on the following line unlike the others. Requesting all to be uniform.--chrom CHROM Chromosome name (String) --in_fasta IN_FASTA Path(s) to new sequence(s) to be inserted into reference genome in fasta format --in_gff IN_GFF Path(s) to GFF file(s) describing new fasta sequence(s) to be inserted --upstream_fasta UPSTREAM_FASTA Path(s) to Fasta file(s) with upstream sequence. Either position, or upstream AND downstream sequence must be provided. --downstream_fasta DOWNSTREAM_FASTA Path(s) to Fasta file(s) with downstream sequence. Either position, or upstream AND downstream sequence must be provided. --position POSITION Comma-separated positions at which to insert new sequence. Note: Position is 0-based, no space between each comma. Either position, or upstream AND downstream sequence must be provided. --ref_fasta REF_FASTA Path to reference fasta file --ref_gff REF_GFF Path to reference gff file