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locks; strict;
comment	@# @;


1.1
date	2018.12.21.19.00.56;	author bacon;	state Exp;
branches;
next	;
commitid	fPsZiwOysvbpoH4B;


desc
@@


1.1
log
@biology/kallisto: import kallisto-0.45.0

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.
@
text
@#!/bin/sh

##########################################################################
#   Script description:
#       Run standard kallisto test data
#       
#   History:
#   Date        Name        Modification
#   2016-03-21  J Bacon     Begin
##########################################################################

usage()
{
    printf "Usage: $0 test-directory\n"
    exit 1
}


##########################################################################
#   Main
##########################################################################

if [ $# != 1 ]; then
    usage
fi

dir="$1"
if [ -e "$dir" ]; then
    printf "$dir already exists.  Remove it first or choose a different name.\n"
    exit 1
fi

cp -iR /usr/local/share/kallisto/test/ "$dir"
cd "$dir"
kallisto index -i transcripts.idx transcripts.fasta.gz
kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
ls -l output
more output/abundance.tsv

cat << EOM

See https://pachterlab.github.io/kallisto/starting.html for instructions
on interpreting the output above.

EOM
@