# salmon_index
Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. The recipe is to build a salmon index for your transcriptome. The script is prepared according to this instruction (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/.)
Recipe source code: https://github.com/rworkflow/ReUseDataRecipe/blob/master/salmon_index.R (opens new window)
Data source: https://salmon.readthedocs.io/en/latest/salmon.html (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| genome | reference genome | File | The fasta file for reference genome |
| transcript | transcripts | File | The fasta file for transcripts from gencode |
# Outputs
| label | type | description | |
|---|---|---|---|
| salmonIdx | salmon index | Directory | A directory containing salmon index files |
# Example:
salmon_index <- recipeLoad('salmon_index.R')
salmon_index$genome <- 'GRCh38.primary_assembly.genome.fa'
salmon_index$transcript <- 'gencode.v42.transcripts.fa'
getData(salmon_index, outdir = 'data/folder', notes = c('salmon_index', 'GRCh38.primary_assembly', 'gencode.v42'))
## Get data from local catch
dataUpdate('data/folder')
dataSearch(c('salmon_index', 'GRCh38.primary_assembly', 'gencode.v42'))