- Align reads to genome and transcriptome using Star
- Count genome mappings using HTSeq
- Count transcript mappings using EdgeR and generate counts
- Generate bigwig files for reads mapping to genome
- Get the code
git clone https://github.com/elswob/rna-seq-pipe.git
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Put all your FASTQ files in a fastq folder and name the folders with the sample names or how you want them.
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Create a txt file called Conditions.txt with folder/sample names and conditions in a tab delimited file
Sample1 Condition1
Sample2 Condition1
Sample3 Condition2
Sample4 Condition2
Sample5 Condition3
Sample6 Condition3
- Check setup - there should be three things in the directory:
- A folder containing the fastq files in separate sample folders with names corresponding to those in conditions file
- A Conditions.txt file as above
- A symlink to the pipeline
- To run the scripts just Run run.sh with the following arguements:
- Number of CPUs
- Species (Mouse or Human)
- Location of a tmp directory
- Location of directory containing samples and fastq files
- Strandedness (reverse, forward or no)
./combined/Run.sh 5 Mouse /path/to/temp/folder/ fastq_folder/ reverse