GitHub - ckenkel/USC_HPC_scripts: a USC-specific set of scripts needed for Tag-Seq and 2bRAD processing

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a USC-specific set of scripts needed for Tag-Seq and 2bRAD processing

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
2bRAD_bowtie2_launch.pl		2bRAD_bowtie2_launch.pl
AlleleFilter.pl		AlleleFilter.pl
BuildRef.pl		BuildRef.pl
CallGenotypes.pl		CallGenotypes.pl
CombineAlleleCounts.pl		CombineAlleleCounts.pl
CombineBaseCounts.pl		CombineBaseCounts.pl
CombineExpression.pl		CombineExpression.pl
CombineReps.pl		CombineReps.pl
CompareSNPMatrices.pl		CompareSNPMatrices.pl
EvalFrags.pl		EvalFrags.pl
ExtractSites.pl		ExtractSites.pl
FastaStats.pl		FastaStats.pl
HRFilterFastq.pl		HRFilterFastq.pl
LowcovSampleFilter.pl		LowcovSampleFilter.pl
MDFilter.pl		MDFilter.pl
OneSNPPerTag.pl		OneSNPPerTag.pl
PolyFilter.pl		PolyFilter.pl
QualFilterFastq.pl		QualFilterFastq.pl
RandomFastq.pl		RandomFastq.pl
RemovePCRDups.pl		RemovePCRDups.pl
RepTagFilter.pl		RepTagFilter.pl
SAMBaseCounts.pl		SAMBaseCounts.pl
SAMFilter.pl		SAMFilter.pl
SAMFilterByGene.pl		SAMFilterByGene.pl
TagTrimmer.pl		TagTrimmer.pl
TruncateFastq.pl		TruncateFastq.pl
adaptors.fasta		adaptors.fasta
batch.sh		batch.sh
countreads.pl		countreads.pl
expression_compiler.pl		expression_compiler.pl
gt2Rqtl.pl		gt2Rqtl.pl
gt2bayes.pl		gt2bayes.pl
gt2colony.pl		gt2colony.pl
gt2dadi.pl		gt2dadi.pl
gt2fasta.pl		gt2fasta.pl
gt2fstat.pl		gt2fstat.pl
gt2phy.pl		gt2phy.pl
gt2related.pl		gt2related.pl
gt2remlf90.pl		gt2remlf90.pl
gt2snpmatrix.pl		gt2snpmatrix.pl
gt2structure.pl		gt2structure.pl
gt2vcf.pl		gt2vcf.pl
iRNAseq_bowtie2map.pl		iRNAseq_bowtie2map.pl
iRNAseq_shrimpmap_SAM.pl		iRNAseq_shrimpmap_SAM.pl
iRNAseq_trim_launch.pl		iRNAseq_trim_launch.pl
iRNAseq_trim_launch0.pl		iRNAseq_trim_launch0.pl
iRNAseq_trim_launch_bgi.pl		iRNAseq_trim_launch_bgi.pl
isogroup_namer.pl		isogroup_namer.pl
job.sh		job.sh
ngs_concat.pl		ngs_concat.pl
organize.sh		organize.sh
rnaseq_clipper.pl		rnaseq_clipper.pl
rnaseq_clipper0.pl		rnaseq_clipper0.pl
rnaseq_clipper_fasta.pl		rnaseq_clipper_fasta.pl
rnaseq_clipper_old.pl		rnaseq_clipper_old.pl
samcount.pl		samcount.pl
samcount_launch.pl		samcount_launch.pl
samcount_launch_bt2.pl		samcount_launch_bt2.pl
samcount_v.0.1.pl		samcount_v.0.1.pl
selectFastaByHeader.pl		selectFastaByHeader.pl
splitFastaByHeader.pl		splitFastaByHeader.pl
tagseq_bowtie2map.pl		tagseq_bowtie2map.pl
tagseq_clipper.pl		tagseq_clipper.pl
tagseq_trim_launch.pl		tagseq_trim_launch.pl
tagseq_trim_launch_bgi.pl		tagseq_trim_launch_bgi.pl