Kallisto HowTo

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Download & Installation

If you are using Linux, download pre-compiled version.

Indexing database

Change $YOUR_PATH, $DB_NAME, and $FASTA to your condition.

  • $KALLISTO - full path to 'kallisto' executable file
  • $DB_NAME - your choice for the database name
  • $FASTA - a database sequence file in FASTA format
 $KALLISTO index -i $DB_NAME $FASTA

Quantification

Change $KALLISTO, $DB_NAME, $FQ1, $FQ2 and $OUT to your condition.

  • $FQ1, $FQ2 - a paired-end FASTQ files
  • $OUT - the name of output directory
  • $THREADS - the number of threads you want to use
  • $LEN_FRAGMENT - Estimated average fragment length (200~400)
  • $STDEV_FRAGMENT Estimated standard deviation of fragment length (0.1)

Paired-end:

  $KALLISTO quant -i $DB_NAME -t $THREADS $FQ1 $FQ2 -o $OUT

Single-end

 $KALLISTO quant --single -l $LEN_FRAGMENT -s $STDEV_FRAGMENT -i $DB_NAME -t $THREADS -o $OUT $FQ1

References