hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples
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- (rev. 1)
- Hyungyong Kim
Structured data
- About
- RNA-seq
- Date Published
- Publisher
- Briefings in Bioinformatics
- URL
- https://www.ncbi.nlm.nih.gov/pubmed/28096075
hppRNA라 불리는 방법을 보고함. 이는 4개의 시나리오로 구성됨.
- pre-mapping
- core-workflow
- post-mapping
- sequence variation detection
그리고, 6개의 독립적인 core-workflow로 구성됨.
- TopHat-Cufflinks-Cuffdiff
- Subread-featureCounts-DESeq2
- STAR-RSEM-EBSeq
- Bowtie-eXpress-edgeR
- kallisto-sleuth
- HISAT-StringTie-Ballgown
이를 Snakemake로 만듬. 핵심 기능은 raw FASTQ 파일을 입력으로 넣어 gene/isoform expression matrix와 DEG, Fusion gene, SNV, lncRNA를 찾는 것.
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