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 |
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).
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:)