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Table 1 Description of main scripts in the QuickRNASeq package

From: QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization

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