txome-pxome-pipeline

Objective

Gernerate fasta files that are derived from RNA-Seq Data for use in peptide-to-protein assignment process

Generate FASTA Databases from Different Sources

1. De novo transcriptome

2. Genome-guided transcriptome

3. Filter on RPKM with CustomProDB Note: SNV proteins are annotated in the fasta headed as where the single amino acid change is indicated:

NP_000009_P65L Indels are annotated in the fasta header as where the insertion or deletion is indicated: NP_001157750_527:ACC>AC

4. Generate variant called database with CustomProDB