[ 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>