[ fxtools sgrna-table
]
Summary
This command will create a table mapping sgRNA names to their parent gene.
Expected Input
This works by parsing the header of each record and currently it expects the header to be as follows:
# {gene}_{auxilliary sgrna description}
Parameters
The command requires an input fasta/q file and will by default write a sgrna-to-gene table to stdout.
You can pipe the output table to a file with the -o
flag.
You can also choose to include each records sequence with the -s
flag.
You can also choose to reorder the columns to whatever format you'd like with the -r
flag
and provide a 3 character string (i.e. -r hsg
or -r ghs
) representing the [hH]eader
,
[sS]sequence
, and [gG]ene
.
By default the table's delimiter is tabs, but you can specify a separate delimiter with the -d
flag.
Usage
fxtools sgrna-table \
-i <input_fastx> \
-o <s2g.txt> \
-s \
-r ghs \
-d <character delim>