nbisweden/lts-a_andersson_2010-mascseq

Repository for long term support project 'Massive and parallel single-cell sequencing of eukaryotic plankton'

A_Andersson_2010-MASCSEQ

Introduction

This repository contains code for primarily RNA-seq analysis for the NBIS long term support project A_Andersson_2010.

Two RNA-seq libraries will be analysed:

NGI ID	User ID	Organism	Mreads	>=Q30(%)
P18363_101	Ph6B	Phaeodactylum tricornutum (diatom)	207.86	95.02
P18363_103	He2B	Heterocapsa sp. (dinoflagellate)	158.81	95.94

Setup

Clone this repository to a convenient place on your computer:

git clone https://github.com/NBISweden/LTS-A_Andersson_2010-MASCSEQ.git

This creates a folder with a copy of all files in the repository; we will refer to this folder as the gwd (github working directory).

Run

We suggest running the analyses in a dedicated folder, here called the awd (analysis working directory), that is different from the gwd.

For convenience, use the wrapper script runSnakemake.sh that encapsulates the snakemake command with necessary options:

bash path/to/runSnakemake.sh [additional options] [optional requested output file]

This sets up a conda environment for snakemake (if needed) and starts the snakemake forkflow. If no optional requested output file] is given, default outfiles will be produced (given by the rule all in Snakefile). It is possible to pass [additional options] to snakemake. One convenient option is the dry-run option -n; this will cause snakemake to show what will be done by the requested analysis, but it will not actually perform it -- very important safety check before running:)