BOL

kallisto can process either single-end or paired-end reads. The default running mode is paired-end and requires an even number of FASTQ files represented as pairs, e.g.

kallisto quant -i index -o output pairA_1.fastq pairA_2.fastq pairB_1.fastq pairB_2.fastq

For single-end mode you supply the --single flag, as well as the -l and -s options, and list any number of FASTQ files, e.g

kallisto quant -i index -o output --single -l 200 -s 20 file1.fastq.gz file2.fastq.gz file3.fastq.gz

FASTQ files can be either plaintext or gzipped.

kallisto quant produces three output files by default:

• abundances.h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length. This file can be read in by sleuth
• abundances.tsv is a plaintext file of the abundance estimates. It does not contains bootstrap estimates. Please use the --plaintext mode to output plaintext abundance estimates. Alternatively, kallisto h5dump can be used to output an HDF5 file to plaintext. The first line contains a header for each column, including estimated counts, TPM, effective length.
• run_info.json is a json file containing information about the run