[ fxtools t2g
]
Summary
This tool can be used to parse a cDNA fasta file and build a mapping of transcripts to genes which is used in Kallisto.
You can decide to include the ensembl gene_id
or the gene_name
which is the common symbol
of that gene.
Usage
# parse the t2g and write to stdout
fxtools t2g -i <your_seq.cdna.fasta.gz>
# parse the t2g and write to `t2g.txt`
fxtools t2g -i <your_seq.cdna.fasta.gz> -o t2g.txt
# parse the t2g and write the symbols instead of the gene_id
fxtools t2g -i <your_seq.cdna.fasta.gz> -s
# parse the t2g and include the gene_id version in the output
fxtools t2g -i <your_seq.cdna.fasta.gz> -s -d