https://github.com/noncodo/ezassembly
All in one script for RNAseq ab initio assembly, mapping, differential expression, and annotation with reference
https://github.com/noncodo/ezassembly
Last synced: 9 months ago
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All in one script for RNAseq ab initio assembly, mapping, differential expression, and annotation with reference
- Host: GitHub
- URL: https://github.com/noncodo/ezassembly
- Owner: noncodo
- Created: 2016-07-12T01:43:56.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2016-08-10T03:28:05.000Z (almost 10 years ago)
- Last Synced: 2025-09-14T03:03:00.864Z (9 months ago)
- Language: Shell
- Size: 10.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# EZassembly
Integrated pipeline for all in one ab initio assembly, mapping, annotation, and differential
expression of RNAseq data when a reference transcriptome is available (reference agnostic).
Requires SGE HPC environment and several common and easy to compile dependencies.
## What it does
Splits up the Trinity pipeline into 3 stages, each using optimal server resources
ensuring that the job finishes quickly, and that you are not monopolosing resources.
Based on this analysis
How to use it:
(1) Copy this folder tree to somewhere in your $HOME or /share
(2) Edit the "custom.cfg" file with some specific parameters in the "Custom Variables"
section (email, group quota, and additional params).
The .cfg file contains information on how to setup your email account to receive SGE
notifications when your job starts and finishes.
(3) Try a 'dry run', like so"
./dynomite.bash ./example/R1_list.txt ./example/R2_list.txt 1 ./trinity_out
(4) Generate the R1.txt and R2.txt files, which contain the full paths of all fastq files
to be assembled (one per line).
for file in /path/to/dir_1/*_R1.fastq /path/to/dir_2/*_R1.fastq; do echo $file ; done > R1.txt
for file in /path/to/dir_1/*_R2.fastq /path/to/dir_2/*_R2.fastq; do echo $file ; done > R2.txt
(5) Run a full job. Example:
./dynomite.bash ./R1.txt ./R2.txt
This will default to 8 CPU (ideal if not trimming) and output written to:
/share/ClusterScratch/your_username/trinity
If your jobs did not complete, you can re-run this script without performing all of the analysis
again as there are builtin recovery checkpoints. However, should you wonder why your jobs didn't
complete, check your output files (TNTpre.oXXXXXX, TNTpre.eXXXXXX, TNT.o/TNT.e/tnt.o/tnt.e).
Some situations often do not produce informative error messages.
Common hard-to-diagnose problems include:
-Using compressed input files (decompress them first);
-Going over quota for RAM (increase the number of CPUs to auto-adjust RAM). This often happens
during the normalization stage.
-Going over quota for # output files (try deleting the "read_components" folder and start over).
This may be problematic with large and complex datasets. If it reoccurs, try using /share/Temp
for your output or contact the sysadmin to request a larger file # quota on ClusterScratch.
Email m.smith@garvan.org.au for help.
N.B. Any custom troubleshooting may require compensation in the form of fermented malt with hops.