An Example of Running TransDecoder

Install of TransDecoder

Referring the website of TransDecoder for details about how to install and run TransDecoder.
https://github.com/TransDecoder/TransDecoder/wiki

Running TransDecoder with example files

We provided example files for running TransDecoder. The files were stored in PATH_OF_PRECISONPRODB/examples/TransDecoder.

PATH_OF_PRECISONPRODB is the location of PrecisionProDB.
PATH_OF_TRANSDECODER is the location of TransDecoder.

# change working directory to example folder
cd PATH_OF_PRECISONPRODB/examples/TransDecoder

# decompress the example files
gzip -d *.gz

# get transcript sequences from the gff file
$PATH_OF_TRANSDECODER/util/gtf_genome_to_cdna_fasta.pl TransDecoder.gtf TransDecoder.genome.fa >TransDecoder.transcripts.fa

# convert gff file to gff3 format
$PATH_OF_TRANSDECODER/util/gtf_to_alignment_gff3.pl TransDecoder.gtf >TransDecoder.gff3

# translate and predict proteins. -m is the minimum length of proteins.
$PATH_OF_TRANSDECODER/TransDecoder.LongOrfs -t TransDecoder.transcripts.fa -m 60
$PATH_OF_TRANSDECODER/TransDecoder.Predict -t TransDecoder.transcripts.fa

# map translated proteins to the genome
$PATH_OF_TRANSDECODER/util/cdna_alignment_orf_to_genome_orf.pl \
                            TransDecoder.transcripts.fa.transdecoder.gff3 \
                            TransDecoder.gff3 \
                            TransDecoder.transcripts.fa > TransDecoder.transcripts.fa.transdecoder.genome.gff3

# to save disk space, compress these files
gzip *

The output files are

• TransDecoder.gff3
• TransDecoder.transcripts.fa
• TransDecoder.transcripts.fa.transdecoder.bed
• TransDecoder.transcripts.fa.transdecoder.cds
• TransDecoder.transcripts.fa.transdecoder.genome.gff3: gff3 annotation based on the genome sequence with proteins.
• TransDecoder.transcripts.fa.transdecoder.gff3: gff3 annotation of proteins based on transcript sequences.
• TransDecoder.transcripts.fa.transdecoder.pep: final result of translated proteins.

Of these files, TransDecoder.transcripts.fa.transdecoder.pep and TransDecoder.transcripts.fa.transdecoder.genome.gff3 are inputs for PrecisonProDB.

You might see some warning messages, which are just normal warning messages.