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RNA Sequencing Tools
| Software | Description | Path |
|---|---|---|
| augustus | ||
| busco | ||
| cufflinks | ||
| express | Expression quantification | /usr/bin/express |
| fastqc | ||
| featurecounts | Counting | /usr/bin/featureCounts |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 |
| kallisto | Expression quantification | /usr/bin/kallisto |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong |
| tophat | ||
| MultiQC | Report Generation | /usr/bin/multiqc |
| RNA-SeQC | QC of RNA-seq alignments. To run this Java program: java -jar /stor/system/opt/rnaseqc/RNA-SeQC_v1.1.8.jar <other options> | /stor/system/opt/rnaseqc |
| hisat | Spliced alignment for mapping RNA-seq reads | /stor/system/opt/hisat-0.1.6-beta |
| hisat2 | Align NGS reads (both DNA and RNA) against a reference genome | /stor/system/opt/hisat2-2.0.5/ |
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