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

easily download fastq file from SRA database requirements:

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

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

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

tMode: trimmomatic
fastqc
multiqc
salmon

working on...

working on...

working on...