kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Version on CSC's Servers
To load the default version on Taito you can use
module load kallisto
For usage help use:
For help on writing batch job scripts see the Taito User Guide.
sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.
To use sleuth:
module load r-env/3.5.1
To use sleuth and kallisto together, load the r-env module first:
module load r-env/3.5.1 module load kallisto
- Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519
- H Pimentel, NL Bray, S Puente, P Melsted and Lior Pachter, Differential analysis of RNA-seq incorporating quantification uncertainty, Nature Methods 14, 687–690 (2017), doi:10.1038/nmeth.4324