MapRnaSeqReadsToGenome

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Begin MapRnaSeqReadsToGenome /Namespace=NgsLib /RunOnServer=False;
Files 
"/Users/administrator/File1_NoIndex_L001.subset.1.fastq.gz 
/Users/administrator/File2_NoIndex_L001.subset.2.fastq.gz"; 
Reference Human.B37; 
GeneModel Ensembl.R65; 
AdapterStripping 3'End /AdapterSequence=TCGTATGCCGTCTTCTGCTTG /ExcludeUnmatched=False;
Trimming /Mode=Composite /LeftTrimming=0 /RightTrimming=0 /ReadTrimQuality=2 /ReadTrimSize=65536; 
Options /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=False /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 
/MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /IndexMode=14Mer /ExcludeNonUniqueMapping=False 
/ReportCutoff=10 /WriteReadsInSeparateFiles=True /OutputFolder="" /GenerateSamFiles=False /ThreadNumber=4 /InsertSizeStandardDeviation=40 
/ExpectedInsertSize=300 /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True 
/ExpressionMeasurement=None /SearchNovelExonJunction=False /SearchTranscriptomeOnly=False /ExcludeUnmappedInBam=False /Version=2 
/ParallelJobNumber=1 /BamSubFolder= /Replace=False /CopyInputFilesToTempDirectory=True
/GroupingFile="/IData_OmicTest/TestGroupFile.txt" /CompressBam=False /CompressBamQualityCutoff=12 /KeepFullRead=False /GenerateBpl=False;
Output ;
End;