Started in March 2020
The RNA-seq pipeline takes in paired-end FASTQ file (gzipped / unzipped), and produced gene count, differential gene expression analysis results, isoform estimation, splicing analysis, promoter motif analysis and pathway analysis. The pipeline was designed to run on SGE cluster.
- trim_galore
- STAR
- Kallisto
- RSEM
- htseq-count
- R
- EdgeR
- DESeq
- Sleuth