RNAseq initial analysis pipeline
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test-fq
test-gz
CNN-RNAseq-clean.R
README.md
runRNAseq-hg19PE.sh
runRNAseq-hg19e.sh
runRNAseq-mm10.sh
runRNAseq-mm10e.sh
runRNAseq-mm9.sh

README.md

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RNAseq analysis pipeline

Michelle Percharde, PhD 2016

michelle.percharde@ucsf.edu

v1.2

###################################################

Script that takes input with name "sample.fq" or "sample.fq.gz" and generates sorted bams Bam files can then be DLed and fed into FeatureCounts in R

 Input files MUST begin .fq.gz or .fq **NOT** .fastq. Rename as necessary

UPDATE 12/07/17: RENAMING. NB all apart from hg19e have transcriptome-aligning now:

runRNAseq-hg19e.sh - hg19 single-end (SE) script with ERCCS
runRNAseq-hg19PE.sh - hg19 paired-end (PE) script
runRNAseq-mm10e.sh - mm10 single-end (SE) script with ERCCS
runRNAseq-mm10.sh - mm10 single-end (SE) script
runRNAseq-mm9.sh - mm9 single-end (SE) script

UPDATE 11/13/17: Added some more scripts. Most recent is runRNAseq-v2.sh. Includes: now aligns to transcriptome(faster), fixed Clontech clipping command,

UPDATE 12/18/16: Tophat working with .gz or .fq files. Currently, alignment is set to mm10 + ERCCs.

FOLDERS NEEDED IN ROOT:

raw/ (where raw files are)

NB: test-fq is a folder of two small, test .fq files that can be used as input folder to check pipeline.


 ### Usage: ./runRNAseq2.sh [-h] [-g] [-c] [-i <path/to/files/>] ###

    -h        Help mode, prints Usage
    -g        Input FASTQ is .gz compressed
    -c        Libraries are CLONTECH
    -i        input file directory/. use ./ for current dir (not recommended)

PIPELINE STEPS

1. trim_galore, fastQC analysis on trimmed files in trimmed/fastqc

2. tophat2, currently set to align to mm10 (+ERCCs)

3. samtools sort

4. exit

KEY NOTES:

  1. Create a sep. dir where raw files are kept. Raw files should end .fq or .gz NOT .fastq

  2. If your file is compressed as .fq.gz, use -g option for correct file nomenclature

  3. If your libraries are clontech, use -c to trim off first 3 repetitive bp

    Good luck!