/rna_seq_analysis_pipeline

Primary LanguageShell

RNA seq analysis (HPC)

Sequence of scripts to run necessary steps to obtain the counts in a bulk sequencing, for both SE and PE samples:

  • QC
  • Preprocesing
  • QC
  • Alignment
  • Quantification

The scripts run each step either in local machine, in an HPC as individual samples, or in an HPC as an arrayjob.

To run the pipeline

1. Create the sample.txt list in DOC and the links to the raw fastq.gz files.

In your own PC:

bash src/00.samples_gen_SE.sh -r ~project_dir//RAW/ -c ~project_dir//DOC/parameters.config

If you want to change the sample names, simply change the print parameters in line 71. Samples names cannot start with a number.

2. Run the QC, trim with cutadapt and do new QC

In the cluster: (ssh user@nodename)

bash /data3/user/src/01.cluster_preprocessing.sh -c ~project_dir//DOC/parameters.config -s se

3. Quantify with rsem / kallisto

In the cluster: (ssh user@nodename)

bash /data3/user/src/02.cluster_quantification.sh -c ~project_dir//DOC/parameters.config -q rsem -t se

4. For PE, we can check the metrics by running

In the cluster: (ssh user@nodename)

bash 03.insert_size_array_job_submission.sh -c ~project_dir/doc/parameters.config

The machine number can be found in in the fastq headers: @HWI-Mxxxx or @Mxxxx - MiSeq
@HWUSI - GAIIx
@HWI-Dxxxx - HiSeq 2000/2500
@Kxxxx - HiSeq 3000(?)/4000
@Nxxxx - NextSeq 500/550
@Axxxxx - NovaSeq