marcottelab/run_msblender

Name: run_msblender

Owner: The Marcotte Lab

Description: null

Created: 2016-12-07 21:23:52.0

Updated: 2016-12-07 21:49:15.0

Pushed: 2017-08-30 19:50:39.0

Homepage: null

Size: 181952

Language: Shell

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README

Wrapper for running MSBlender for an experiment with multiple mxZMLs

Works with the MSBlender branch MSblender_restructure

On TACC or not TACC

Setup experiment directory

Start with a folder for each experiment containing a folder called mzXML containing its mzxml files and a folder called DB containing formatted fasta database. See below for how to make a formatted fasta

Structure of an experiment directory for experiment Ce1104

Ce1104_example

—–mzXML

———- WAN1100427_OT2_Celegans_HCW_P1A01.mzXML

———- WAN1100427_OT2_Celegans_HCW_P1A02.mzXML

—–DB

———- uniprot-proteome%3AUP000001940_caeel_contam.combined.fasta

Write each experiment you want to process as one line in a list of experiment IDs

This can be a one line file with one experiment or multiline with multiple experiments

For example:

t exp_list_example.txt
04_example

Create additional folders in the experiment directory

sh scripts/create_directory.sh $SCRATCH/metazoans/exp_list_example.txt

Format msblender commands for each mzXML in the experiments

Creates file for each experiment called [experimentID]_commands.txt

sh scripts/create_commands.sh exp_list_example.txt $WORK/MSblender/runMS2.sh $HOME/searchgui

Create the TACC job submission script to process the commands in parallel

Need to manually edit header in template_run_MS.sbatch

Creates file for each experiment called [experimentid]_run_MS.sbatch

sh scripts/create_sbatch.sh exp_list_example.txt

atch Ce_1104_example_run_MS.sbatch

If not on TACC, process the commands with parallel

rallel -j4 :::: Ce1104_COMMANDS.txt

Format fasta DB

This goes in /DB folder of each experiment

Can also format ahead of time for a proteome and just cp in to the DB folder

Add on contaminants and reverse proteome

sh $WORK/MSblender/setup/setup_database_only.sh uniprot-triticum%3AUP000019116.fasta

Generate blast formatted db

rmatdb -i uniprot-triticum%3AUP000019116_contam.combined.fasta