hsiehph / transcript2genemodel

Transcript2GeneModel

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