| Progress | Process Name |
|---|---|
| ☑ | FastQC |
| ☑ | Fastqmcf |
| ☑ | FastQC(trimmed) |
| ☑ | Hisat2 (All genes) |
| ☑ | Hisat2 (rRNA) |
| ☑ | Hisat2 (SIRVome) |
| ☑ | RSEM (All genes) |
| ☑ | RSEM (SIRVome) |
| ☑ | Bam to BigWig |
| ☑ | adjust_bed_noncoding |
| ☑ | RSeQC(read_distribution.py, infer_experiment.py, junction_annotation.py, inner_distance.py) |
| ☑ | readcoverage.jl (All genes) |
| ☑ | readcoverage.jl (SIRV genes) |
| ☑ | FeatureCounts (All-genes GTF) |
| ☑ | output TPMCounts |
| ☑ | FeatureCounts (Mitochondrial GTF) |
| ☑ | FeatureCounts (rRNA GTF) |
| ☑ | FeatureCounts (Histone GTF) |
| ☑ | edgeR MDS and heatmap |
| ☑ | ERCC corr barplot |
| ☑ | Assigned to genome rate barplot |
| ☑ | FeatureCounts mapped rate barplot(allgene, mt, histone) |
| ☑ | Create plots from TPM counts (num of detected genes, dimentianl reduction) |
| ☑ | Create plots from RSEM TPM counts (num of detected genes, num of detected transcripts) |
| ☑ | SIRV entropy barplot |
| ☑ | MultiQC Report |
| ☑ | helpMessage() |
| ☑ | get_software_versions() |