salmon_partial_sa_index (version: 0.0.1)
Output asset class: salmon_partial_sa_index
Description: Transcriptome index for salmon, produced with salmon index using partial selective alignment method. Preparation includes transcriptome mapping to the genome and extraction of the relevant portion out from the genome and indexing it along with the transcriptome. Recipe source -- https://github.com/COMBINE-lab/SalmonTools/blob/master/scripts/generateDecoyTranscriptome.sh
Inputs
| Type | Name | Description | Default |
|---|---|---|---|
| assets | ensembl_gtf (gtf) | GTF file for exonic features extraction | ensembl_gtf |
| assets | fasta (fasta) | fasta asset for genome | fasta |
| assets | fasta_txome (fasta) | fasta asset for transcriptome | fasta_txome |
| params | kmer | The length of kmer to use to create the indices | 31 |
| params | threads | Number of threads to use for parallel computing | 8 |