Quantify abundances of the transcripts using the two read files reads_1.fastq.gz and reads_2.fastq.gz (the .gz suffix means the read files have been gzipped; kallisto can read in either plain-text or gzipped read files).
kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
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