| Sailfish is a tool for transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads. Sailfish runs in two phases; indexing and quantification. The indexing step is independent of the reads, and only needs to be run once for a particular set of reference transcripts and choice of k (the k-mer size). The quantification step, obviously, is specific to the set of RNA-seq reads and is thus run more frequently Additional covariates may optionally be provided to further inform the peak-calling process. https://github.com/kingsfordgroup/sailfish |
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/sailfish
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| transcript quantification from RNA-seq data | 0.10.1.1 | any | |