RNA-seq¶
Check Reads check_reads¶
| input: | List of read files (.fastq) |
|---|---|
| output: | None |
| script: | Ensures correct format of sequencing read files |
Genome Indexing hisat_indexing/star_indexing¶
| input: | Genome reference file (.fa) | Genome annotation file (.gtf) |
|---|---|
| output: | Directory containing indexed genome files |
| script: | Uses either STAR or HISAT2 to build an indexed genome |
Pre-Quality Check pre_fastqc¶
| input: | List of read files (.fastq) |
|---|---|
| output: | Report files (.html) |
| script: | Uses FastQC to check quality of read files |
Pre-MultiQC pre_multiqc¶
| input: | Log files (.log) |
|---|---|
| output: | Summary report file (.html) |
| script: | Uses MultiQC to generate a summary report |
Read Trimming trim_galore¶
| input: | List of read files (.fastq) |
|---|---|
| output: | Trimmed read files (.fastq) | Report files (.html) |
| script: | Trims low quality reads with TrimGalore and checks quality with FastQC |
Read Mapping hisat_mapping/star_mapping¶
| input: | List of read files (.fastq) | Genome annotation file (.gtf) | Directory containing indexed reference genome files |
|---|---|
| output: | A list of alignment files (.bam) | Log files (.log) |
| script: | Uses either STAR or HISAT2 to align reads to a reference genome |
Reformat Reference gtftobed¶
| input: | Genome annotation file (.gtf) |
|---|---|
| output: | Genome annotation file (.bed) |
| script: | Converts genome annotation file from GTF to BED format |
Mapping Quality rseqc¶
| input: | A list of alignment files (.bam) |
|---|---|
| output: | Report files (.txt) |
| script: | Uses RSeQC to check quality of alignment files |
Quantification counting¶
| input: | A list of alignment files (.bam) | Genome annotation file (.gtf) |
|---|---|
| output: | Read counts (.txt) | Log files (.txt) |
| script: | Uses either StringTie, HTSeQ, or featureCounts to quantify reads |
Expression Matrix expression_matrix¶
| input: | A list of count files (.txt) |
|---|---|
| output: | An expression matrix (.txt) |
| script: | Reformats a list of count files into a genes x samples matrix |
Expression Features expression_features¶
| input: | Genome annotation file (.gtf) | An expression matrix (.txt) |
|---|---|
| output: | Gene feature data (.txt) |
| script: | Parses the genome annotation file for gene feature data |
Expression Set expression_set¶
| input: | An expression matrix (.txt) | Gene feature data (.txt) | Sample phenotypic data (.txt) |
|---|---|
| output: | An expression set object (.rds) |
| script: | Creates an expression set object with eData, fData, and pData attributes |
Summary Report multiqc¶
| input: | Log files and summary reports from all processes |
|---|---|
| output: | A summary report (.html) |
| script: | Uses MultiQC to generate a summary report |