In b97jre/RNAmappingPipeline: GBP sequence data throughput

RNA-seq pipeline info

This is the instruction for how to run this RNAseq pipeline on your data. It requires some manual steps which will be described below. The pipeline is divided in two parts. The first will map all the reads to a reference and then create a table with all the count reads in one table.The second will generate a QC report for your data and generate a html file and a pdf file of all the quality measurments. All paths written in this report is done for running on uppmax but all the programs and files can be found on github

RNA-seq pipeline setup

Step by step procedure how to setup and start the pipeline

To run the pipeline you will have to fill in some information regarding your project. This is done in some steps.

1. Create folder where you want to run your pipline
   • mkdir workFolder

2. Go into folder and initiate the setup

   • cd workFolder
   • java -jar /glob/johanr/bin/RNAseqSetup.jar

3. The program will now look for two files. The first is named parameters.table.txt and will contain information on different files and parameters that will be used during the mapping procedure. The second is named metaData.table.tab.txt and contains information on all the samples that will be included in the mapping and also additional information regarding the samples. Since none of the files have been generated the first file parameters.table.txt will be generated. More information on how to fill in the table se below

4. Once the parameters.table.txt is correctly filled in restart the setup
   • java -jar /glob/johanr/bin/RNAseqSetup.jar
5. The information given in parameters.table.txt regarding the samples will be used to identify all the reads that will be used in the mapping pipeline and written down in the metaData.table.tab.txt. Make sure you change the metaData.table so that the sampleNames make sense and that as much of the meta data is filled in. More information on how to fill in the metaData.table.tab.txt see below
6. Once the metaData.table.tab.txt is correctly filled in restart the setup
   • java -jar /glob/johanr/bin/RNAseqSetup.jar
7. This will now create a correct directory structure and create soft links for all the files that will be used in the analysis. After that you will have the choice to either start the pipeline, write a report with all the setupinformation or abort the setup
   • y will start the pipeline and write a report with all parameters and settings and all the samples with its metadata.
   • n will write a report with all parameters and settings and all the samples with its metadata.
   • x will quit the setup.

Code example of setup

The most importan thing during setup is to actually change the values in the two files parameters.table.txt and metaData.table.tab.txt

#create work directory
mkdir workdir

# go into work directory
cd workdir

# Initiate setup
java -jar /glob/johanr/bin/RNAseqSetup.jar

#Change in parameters.table.txt
vim parameters.table.txt

# Use info in  parameters.table.txt find all reads associated to generate the correct metadata info
java -jar /glob/johanr/bin/RNAseqSetup.jar

#Change in sampleNames in metaData.table.tab.txt and add metadata info on the samples
vim metaData.table.tab.txt

#Start the pipeline
java -jar /glob/johanr/bin/RNAseqSetup.jar

b97jre/RNAmappingPipeline documentation built on May 11, 2019, 5:22 p.m.