Generate and run OmicScript in ArrayStudio GUI

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If you have ArrayStudio, the best way to generate OmicScript is by clicking the “show script” button. You will get the latest OmicScript parameter setting from the GUI.

Example of generating RNA-Seq alignment OmicScript.


Take the “map RNA-Seq Reads to Genome” function as one example (see figure on right). You will get Script similar to below (always get the latest oscript from GUI):


Begin MapRnaSeqReadsToGenome /Namespace=NgsLib;
Files
"/test/testdata/SimulatedReads_1.fastq.gz
/test/testdata/SimulatedReads_2.fastq.gz";
Reference Human.B37.3;
GeneModel RefGene;
Trimming /Mode=TrimByQuality /ReadTrimQuality=2;
Options /ParallelJobNumber=1 /PairedEnd=True /FileFormat=AUTO /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=True /MaxMiddleInsertionSize=10 
/MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /IndexMode=14Mer /ExcludeNonUniqueMapping=False /ReportCutoff=10 
/WriteReadsInSeparateFiles=True /OutputFolder="/test/BAMFile" /GenerateSamFiles=False /ThreadNumber=12 
/InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic 
/CompressionMethod=Gzip /Gzip=True /ExpressionMeasurement=None /SearchNovelExonJunction=True /ExcludeUnmappedInBam=False;
Output RNASeq;

Running in opened projects in ArrayStudio/ArrayServer

You can manually modify these script options. If you have ArrayStudio software, you can run the entire script by:

Run script in GUI

If you are using Server projects. Make sure your script has "/RunOnServer=True" and using "Run Script (Send to Queue)".

Running in Oshell as a fresh project

If you are running in Oshell as a fresh project, you can wrap the RNA-Seq alignment script with NewProject (create the environment) and SaveProject, CloseProject to close the environment, the complete script will look like below:

Begin NewProject;
File "/test/omicsoft/test1.osprj";
Options /Distributed=True;
End;
 
Begin MapRnaSeqReadsToGenome /Namespace=NgsLib;
Files
"/test/testdata/SimulatedReads_1.fastq.gz
/test/testdata/SimulatedReads_2.fastq.gz";
Reference Human.B37.3;
GeneModel RefGene;
Trimming /Mode=TrimByQuality /ReadTrimQuality=2;
Options /ParallelJobNumber=1 /PairedEnd=True /FileFormat=AUTO /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=True /MaxMiddleInsertionSize=10 
/MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /IndexMode=14Mer /ExcludeNonUniqueMapping=False /ReportCutoff=10 
/WriteReadsInSeparateFiles=True /OutputFolder="/test/BAMFile" /GenerateSamFiles=False /ThreadNumber=12 
/InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic 
/CompressionMethod=Gzip /Gzip=True /ExpressionMeasurement=None /SearchNovelExonJunction=True /ExcludeUnmappedInBam=False;
Output RNASeq;
 
Begin SaveProject;
Project test1;
File "/test/omicsoft/test1.osprj";
End;
 
Begin CloseProject;
Project test1;
End;

Or run the script in Oshell or modify it with parameters and add to Server Script.