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Akshay Paropkari edited this page Feb 17, 2020 · 1 revision

RNAseq Wiki

This wiki is a user guide covering the usage of the RNAseq pipeline implemented in this repository. UC Merced researchers working with 3’mRNA-Seq data can utilize this pipeline on the MERCED cluster. Please refer to the requirements section before proceeding to the next page.

Requirements

  1. MERCED login information. See more information on getting a MERCED account
  2. Basic knowledge of Linux. See more information on general Linux resources
  3. Raw FASTQ sequencing data
  4. Sample metadata

Table of contents

  1. Introduction
  2. Accessing MERCED cluster
  3. Loading RNAseq environment
  4. Creating input data folder
    1. Transferring data to/from MERCED to a local machine
  5. Running RNAseq pipeline as a MERCED job
    1. Overview
    2. Required changes to the job template file
    3. Example of changed job template file
    4. Submitting jobs to MERCED
  6. Output files

Quick Access

  1. Introduction
  2. Accessing MERCED cluster
  3. Loading RNAseq environment
  4. Creating input data folder
    1. Transferring data to/from MERCED to a local machine
  5. Running RNAseq pipeline as a MERCED job
    1. Overview
    2. Required changes to the job template file
    3. Example of changed job template file
    4. Submitting jobs to MERCED
  6. Output files
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