head 1.1; access; symbols pkgsrc-2023Q4:1.1.0.42 pkgsrc-2023Q4-base:1.1 pkgsrc-2023Q3:1.1.0.40 pkgsrc-2023Q3-base:1.1 pkgsrc-2023Q2:1.1.0.38 pkgsrc-2023Q2-base:1.1 pkgsrc-2023Q1:1.1.0.36 pkgsrc-2023Q1-base:1.1 pkgsrc-2022Q4:1.1.0.34 pkgsrc-2022Q4-base:1.1 pkgsrc-2022Q3:1.1.0.32 pkgsrc-2022Q3-base:1.1 pkgsrc-2022Q2:1.1.0.30 pkgsrc-2022Q2-base:1.1 pkgsrc-2022Q1:1.1.0.28 pkgsrc-2022Q1-base:1.1 pkgsrc-2021Q4:1.1.0.26 pkgsrc-2021Q4-base:1.1 pkgsrc-2021Q3:1.1.0.24 pkgsrc-2021Q3-base:1.1 pkgsrc-2021Q2:1.1.0.22 pkgsrc-2021Q2-base:1.1 pkgsrc-2021Q1:1.1.0.20 pkgsrc-2021Q1-base:1.1 pkgsrc-2020Q4:1.1.0.18 pkgsrc-2020Q4-base:1.1 pkgsrc-2020Q3:1.1.0.16 pkgsrc-2020Q3-base:1.1 pkgsrc-2020Q2:1.1.0.14 pkgsrc-2020Q2-base:1.1 pkgsrc-2020Q1:1.1.0.10 pkgsrc-2020Q1-base:1.1 pkgsrc-2019Q4:1.1.0.12 pkgsrc-2019Q4-base:1.1 pkgsrc-2019Q3:1.1.0.8 pkgsrc-2019Q3-base:1.1 pkgsrc-2019Q2:1.1.0.6 pkgsrc-2019Q2-base:1.1 pkgsrc-2019Q1:1.1.0.4 pkgsrc-2019Q1-base:1.1 pkgsrc-2018Q4:1.1.0.2 pkgsrc-2018Q4-base:1.1; 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 @