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omics-pipeline: pipelines for various omics analysis

Usage:

git clone https://github.com/CadenZhao/omics-pipeline.git
cd omics-pipeline/omxpipeline

# use -h flag to check the usage
./SRAdownload-pipeline.py -h
./bulkRNA-pipeline.sh -h
<path to pipeline> -h

Pipeline description

1. SRAdownload-pipeline.sh

easily download fastq file from SRA database requirements:

1. sra-toolkit (should include fasterq-dump)
2. SraRunTable.txt (downloaded from SRA database)

2. bulkRNA-pipeline.sh

QC, alignment, gene count, gene TPM, BAM to BigWig

Requirements:

gMode: trimmomatic
fastqc
multiqc
STAR
samtools
R (with GenomicFeatures package)

tMode: trimmomatic
fastqc
multiqc
salmon

3. scRNA-pipeline.sh

working on...

4. ChIPseq-pipeline.sh

working on...

5. WGS-pipeline.sh

working on...