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Jit bookmarked kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq dataComments- BioStar 2131 days ago
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.fastqFor single-end mode you supply the
--singleflag, as well as the-land-soptions, and list any number of FASTQ files, e.gkallisto quant -i index -o output --single -l 200 -s 20 file1.fastq.gz file2.fastq.gz file3.fastq.gzFASTQ files can be either plaintext or gzipped.
kallisto quantproduces 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
--plaintextmode to output plaintext abundance estimates. Alternatively,kallisto h5dumpcan 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
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