| title | author | date | output | vignette |
|---|---|---|---|---|
CS cluster RNAseq tutorial |
Cristina Venturini |
`r Sys.Date()` |
rmarkdown::html_vignette |
%\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}
|
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
First, you need to connect to the cluster. Options:
-
Putty (for Windows)
-
Mac/Linux: open terminal:
ssh <userid>@bchuckle.cs.ucl.ac.uk
Some useful unix/bash commands:
ls -lhrt #list dir contents
mkdir tutorial #make a new dir called "tutorial"
cd tutorial #change to dir "tutorial"
pwd #check your current dir
Download the tutorial from github:
Prepare the data:
nano samples.tab #copy and paste your samples here. To come out: ctrl+x, press "Y"
perl -lane 'print $F[0],"",$F[1],"*"' data/samples.tab > data/samples_todownload.tab #add * after each sample
nano scripts/getting_data_RSD.sh #change user id
sh scripts/getting_data_RSD.sh #this will download data from RSD storage. You will be prompted to insert your password twice - NB.it's your RSD/UCL password, not the CS cluster one!
Create index (only needed at the beginning or when it changes - now we are at release 94)
wget -O data/Homo_sapiens.GRCh38_rel94.cdna.all.fa.gz 'ftp:https://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz'
nano scripts/making_index.sh #change user id/ dir
mkdir ref
mkdir ref/cluster
qsub scripts/making_index.sh #submit the job - the job will go into a queue and then start to run
qstat #to check your job: qw - waiting in the queue; r - running; Eqw - some problems!
Run kallisto
Get temp cmp and tpm matrix First time you run this:
/share/apps/R-3.5.1/bin/R
#copy and paste this and follow instruction for personal library
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
#then copy and paste this:
BiocManager::install("tximport", version = "3.8") #tximport
BiocManager::install("biomaRt", version = "3.8") #biomart
install.packages("reshape","dplyr")
#to exit type: q()
cd results/
/share/apps/R-3.5.1/bin/R CMD BATCH ../scripts/processing_rnaseq_step2.r