This is a simple snakemake pipeline to predict gene models from genomic DNA (FASTA sequences) using transcripts (i.e., this is a transcript-guided approach).
Note, this pipeline will only work on the Eichler lab cluster due to dependencies
First, you will need to clone this repo.
git clone [email protected]:hsiehph/Transcript2GeneModel.git
**** The config.yaml must contain correct paths to the files for transcripts and FASTA sequences. ****
To run this pipeline,
snakemake --drmaa " -V -cwd -w n -e ./log -o ./log {params.sge_opts} -S /bin/bash" -j 20 -w 60 -s findORF.snake
The predicted gene models are listed in the output BED file.
./output/haplotypeID/haplotypeID.tsv.ORFs.final.cds.bam.bed
The predicted peptide sequences are listed in the output pep file.
./output/haplotypeID/haplotypeID.tsv.ORFs.final.pep