Table 1.
Description of main scripts in the QuickRNASeq package
| Script | Function |
|---|---|
| star-fc-qc.sh | Master script for Step #1 in Fig. 1 |
| star-fc-qc.ws.sh | Same as star-fc-qc.sh, but implemented for a standalone workstation |
| star-fc-qc.summary.sh | Master script for Step #2 in Fig. 1 |
| get-star-summary.pl | Merge STAR mapping summary |
| get-fc-summary.pl | Merge featureCounts counting summary |
| get-read-dist.pl | Merge read distribution from RSeQC |
| get-snp-corr.pl | Calculate all-against-all pairwise SNP correlations |
| get-expr-table.R | Merge counts table from individual samples |
| get-expr-qc.R | Perform correlation-based QC, and calculate normalization factor |
| plot-rnaseq-metrics.R | Plot the summaries for read mapping, counting, or read distribution |
| plot-corr-matrix.R | Plot a correlations matrix |
| plot-expr-count.R | Plot the number of genes with varying RPKM cut-offs |
| RSeQC-html.pl | Generate a HTML QC report for individual sample |
| make_HTMLs.sh | Generate a comprehensive, integrated, and interactive project report |
| gtf2annot.pl | Utility to extract gene annotation from a GTF file |
| gtf2bed.pl | Utility to convert a gene annotation from GTF to BED format |
| star-fc-qc.config.template | Template configuration file for customization |