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commands_executed
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####----------------Here a list of commands executed for the RiboTaper analysis.(version 1.2, November 2015)------------------
###################################################################
# This file is part of RiboTaper.
# RiboTaper is a method for defining traslated ORFs using
# Ribosome Profiling data.
#
# Copyright (C) 2015 Lorenzo Calviello
#
# RiboTaper is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# RiboTaper is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with RiboTaper. If not, see <http://www.gnu.org/licenses/>.
#
# Contact: [email protected]
#######################################################################
####Unpack the provided files on our website (https://ohlerlab.mdc-berlin.de/software/):
#alignment_files.tar.gz
#annotation_human_daniorerio.tar.gz
#RiboTaper_v1.0.tar.gz
tar -zxvf alignment_files.tar.gz
tar -zxvf annotation_human_daniorerio.tar.gz
tar -zxvf RiboTaper_v1.0.tar.gz
#### create annotation files for human using ccds and appris tags (Gencode 19 + hg19 genome):
scripts/create_annotations_files.bash annotation_human_daniorerio/gencode.v19.annotation.gtf annotation_human_daniorerio/hg19_genome.fa true true annotation_dir_human bedtools_dir/ scripts/
#### create annotation files Danio rerio created without using any tags (no ccds, no appris):
scripts/create_annotations_files.bash annotation_human_daniorerio/Danio_rerio.Zv9.76_noscaff.gtf annotation_human_daniorerio/Danio_rerio.Zv9.dna.toplevel_noscaff.fa false false annotation_dir_zebr bedtools_dir/ scripts/
#### create new directories for the provided experiments
mkdir HEK_this_study HEK_Gao Zebrafish_Bazzini_5hPF
### go inside the first directory
cd HEK_this_study
### submit bash script for SGE computing, using 7 cores and 8 Gigabyte of RAM per core
### HEK293 data for this study, Ribo-seq newly generated + RNA seq from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49831
### annotation files from human
qsub ../commands/ribotaper_this_study.q
### go inside the second directory
cd ../HEK_Gao
### submit bash script for SGE computing, using 7 cores and 8 Gigabyte of RAM per core
### HEK293 data for Gao et al, cycloheximide (Ribo) and RNA-seq experiments for the "control" sample: http://www.ncbi.nlm.nih.gov/sra/SRX740748%5Baccn%5D http://www.ncbi.nlm.nih.gov/sra/SRX740751%5Baccn%5D
qsub ../commands/ribotaper_Gao.q
### go inside the third directory
cd ../Zebrafish_Bazzini_5hPF
### Danio Rerio data for 5h_PF, from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53693
### submit bash script for SGE computing, using 7 cores and 8 Gigabyte of RAM per core
qsub ../commands/ribotaper_Zebr.q