Galaxy |

Kallisto quant (version 0.48.0+galaxy1)

Reference transcriptome for quantification:

Select a reference transcriptome:

If your transcriptome of interest is not listed, contact your Galaxy administrator

Single-end or paired reads:

Reads in FASTQ format:

Average fragment length:

Illumina typically produces reads of 180-200bp

Estimated standard deviation of fragment length:

Perform sequence based bias correction:

It allows to learn parameters for a model of sequences specific bias and corrects the abundances accordlingly

Number of bootstrap samples:

Running with bootstraps is mandatory if you want to perform differential expression analysis of isoforms with Sleuth.Default: 0

Search for fusions:

It generates the required files for Pizzly. This option does normal quantification, but additionally looks for reads that do not pseudoalign because they are potentially from fusion genes.

Single overhang:

Include reads where unobserved rest of fragment is predicted to lie outside a transcript

Output pseudoalignments in BAM format:

Project pseudoalignments to genome:

Seed for the bootstrap sampling:

Default: 42

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. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.