Sailfish index + quant - Githubissues

YeoLab / flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data

http://yeolab.github.io/flotilla/docs

BSD 3-Clause "New" or "Revised" License

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Sailfish index + quant #1

Closed olgabot closed 10 years ago

olgabot commented 10 years ago

These features should make it dead simple to create a sailfish index and run sailfish on TSCC, without having to write up the submitter yourself. Should deal with single-end and paired end reads.

sailfish_index.py

Given a fasta file (or a bunch of fasta files), or a fa.gz file, and a kmer size k, submit a job to tscc and create an index

sailfish_quant.py

Given a bunch of fastq files (or fastq.gz files), as in a file list the exact same as accepted by the GATK queue pipeline, run sailfish quant with reasonable defaults (where "reasonable" is to be determined)
- does this need to be gencode_v17 standard for encode?

olgabot commented 10 years ago

mixed up flotilla and gscripts repos