1) Building the STAR indexes:
	A) genome:
		cp buildStarGenomicIndex.qsub
		Input:
			c_elegans.PRJNA13758.WS245.genomic.renamed.fa
			WS245.exons.sort.renamed.gff3
		
	B) transcriptome:		
		buildStarIndexFromGFF.qsub
		Input:
			WS245TranscriptomeFromGFF.fasta
		
2) Alignment of fastq:
	Directory: AlignQsubs

3) Merging alignments of same library
	Directory: MergeQsubs

4) Calculate duplication rates
	Directory: CalcDupRateQsubs

5) Removing PCR duplicates
	Directory: RemoveDupQsubs

6) Count mapped reads after duplicates removed (Genomic,Transcriptomic,rRNA) 
	Directory: ReadCountQsubs

7) Form alignments of unique mappers (multi-mappers removed) 
	Directory: UniqueReadQsubs

8) Exclude reads that overlap introns based on WS260 gene model, count reads for the set of non-overlapping exons 
	Input: NonOverlappingExons.gff3
	Directory: ExonCountQsubs

9) Build BedGraph and BigWig files for UCSC trackhub construction 
	Input: ce11.chrom.sizes
	Directory: BigWig
	Programs:
		org.rhwlab.LMS.RNASeq.merged.MergedID in LabManagement.jar
		bam2wig.jar
		wigToBigWig
		bigWigToBedGraph
		
10) Calculate gene read counts using HTSeq
	Directory: HTSeqQsubs
	
11) Calculate transcript and gene TPM using BitSeq
	Input: mRNA.pseudo.xome.fa
	Directory: BitSeq

12) JAVA programs (source and executable)
	Directories:
		JavaPrograms/Labmanagment
		Javaprograma/modernlib
		JavaPrograms/RHW_DB	

13) Gene Coregulation Analysis 
	Program: org.rhwlab.LMS.dataframe.coreg.CoregulationFrame in Labmanagement.jar

14) ChipSeq enrichment of DE genes 
	Programs:
		org.rhwlab.encode.ChipSeq.peaks.ClusterEnrichment in modernlib.jar	
		org.rhwlab.encode.ChipSeq.peaks.EnrichmentHeatmap in modernlib.jar
	Input:			
		Embryonic_LarvalPeakClusters.tab
		gene_diffexpress.yes_exclude.180130.txt
		DEGeneEnrichment/
	
16) Gene Clustering investigation  
	Input: facsFuzzy.xml
	Program: org.rhwlab.LMS.dataframe.investigator.InvestigationFrame in RHW_DB.jar

17) Program versions used:
	samtools   1.9
	STAR       2.4.2a
	BitSeq     1.16.0
	java       1.8.0_102
	python     3.5.2
	HTSeq      0.9.1
	numpy      1.13.1
	pysam      0.11.2.2
	python_Levenshtein 0.12.0
	R          3.3.0
