Transcriptome_resequencing_report
|-- BGI_result		[ All result files of project are stored in this folder except clean fq file and bam file (if you do IGV visualication) because they are very large. Most of these result files are displayed in webpage report and you can refer to help manual section in report to get more methods and file format description ]
|   |-- 0.Abstract	[ Brief statistics of the whole project, based on files on other result folders]
|   |   |-- diff.statistics.xls
|   |   |-- project_info.txt
|   |   |-- project_info_en.txt
|   |   `-- sample.statistics.xls
|   |-- 1.CleanDataAssess	[All result files that related to clean data assess are stored in this folder]
|   |   |-- sample1
|   |   |   |-- [LaneID_of_sample1].base.png
|   |   |   |-- [LaneID_of_sample1].qual.png
|   |   |   |-- sample1.RawReadsClass.pdf
|   |   |   |-- sample1.RawReadsClass.png
|   |   |   `-- sample1.xls
|   |-- 2.MappingAssess		[ All result files that related to alignment assess are stored in this folder ]
|   |   |-- MapStatistics　　　　
|   |   |   |-- sample1.Bowtie2Gene.MapReadsStat.xls
|   |   |   `-- sample1.Bwa2Genome.MapReadsStat.xls
|   |   `-- ReadsRandom
|   |       |-- sample1.ReadsRandom.pdf
|   |       `-- sample1.ReadsRandom.png
|   |-- 3.QuantitativeAnalysis　　[ All result files that related to quantitative analysis of each sample are stored in this folder ]
|   |   |-- ExonExp		
|   |   |   |-- sample1.exonCov.pdf
|   |   |   |-- sample1.exonCov.png
|   |   |   `-- sample1.exonexpr.xls
|   |   |-- GeneAndIsoformExp	
|   |   |   |-- sample1.gene.FPKM.xls
|   |   |   |-- sample1.isoform.FPKM.xls
|   |   |   |-- all.gene.FPKM.xls
|   |   |   `-- all.isoform.FPKM.xls
|   |   |-- GeneConditionSpecifity	
|   |   |   |-- sample1.spe_gene.xls
|   |   |   `-- spc_gene.png
|   |   |-- GeneCorStatAndVenn		
|   |   |   |-- Heatmap
|   |   |   |   |-- All.CorrelationHeatmap.pdf
|   |   |   |   |-- All.CorrelationHeatmap.png
|   |   |   |   `-- All.correlation.stat.xls
|   |   |   |-- Tree
|   |   |   |   |-- All.HclustTree.pdf
|   |   |   |   `-- All.HclustTree.png
|   |   |   `-- Venn
|   |   |       |-- venn_sample1-vs-HBRR2-vs-HBRR3.pdf
|   |   |       `-- venn_sample1-vs-HBRR2-vs-HBRR3.png
|   |   |-- GeneDiff
|   |   |   |-- sample2-VS-sample1.GeneDiffExp.png
|   |   |   |-- sample2-VS-sample1.GeneDiffExp.xls
|   |   |   |-- DEGstat.pdf
|   |   |   `-- DEGstat.png
|   |   |-- GeneDiff_Function
|   |   |   |-- Cluster
|   |   |   |   |-- META-INF
|   |   |   |   |-- TreeView.jar
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.atr
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.cdt
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.data
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.gtr
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.pdf
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.png
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.inter.xls
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.atr
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.cdt
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.data
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.gtr
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.pdf
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.png
|   |   |   |   |-- sample2-VS-sample1.UHRR2-VS-HBRR2.union.xls
|   |   |   |   |-- cluster.html
|   |   |   |   |-- cluster_en.html
|   |   |   |   |-- coordinates
|   |   |   |   |-- gpl.txt
|   |   |   |   |-- images
|   |   |   |   |-- lib
|   |   |   |   |-- plugins
|   |   |   |   |-- setup.exe
|   |   |   |   |-- win32TreeView.bat
|   |   |   |   `-- windows
|   |   |   |-- GO
|   |   |   |   |-- GOView.html
|   |   |   |   |-- GOViewList.html
|   |   |   |   |-- META-INF
|   |   |   |   |-- TreeView.jar
|   |   |   |   |-- sample2-VS-sample1.GO2gene.xls
|   |   |   |   |-- sample2-VS-sample1.glist
|   |   |   |   |-- sample2-VS-sample1.goclass.png
|   |   |   |   |-- sample2-VS-sample1.goclass.svg
|   |   |   |   |-- sample2-VS-sample1_C.html
|   |   |   |   |-- sample2-VS-sample1_C.png
|   |   |   |   |-- sample2-VS-sample1_C.txt
|   |   |   |   |-- sample2-VS-sample1_F.html
|   |   |   |   |-- sample2-VS-sample1_F.png
|   |   |   |   |-- sample2-VS-sample1_F.txt
|   |   |   |   |-- sample2-VS-sample1_P.html
|   |   |   |   |-- sample2-VS-sample1_P.png
|   |   |   |   |-- sample2-VS-sample1_P.txt
|   |   |   |   |-- cluster
|   |   |   |   |-- coordinates
|   |   |   |   |-- gpl.txt
|   |   |   |   |-- images
|   |   |   |   |-- lib
|   |   |   |   |-- plugins
|   |   |   |   |-- setup.exe
|   |   |   |   |-- win32TreeView.bat
|   |   |   |   `-- windows
|   |   |   |-- Network
|   |   |   |   |-- 9606.medusa
|   |   |   |   |-- Cytoscape.Usage_en.pdf
|   |   |   |   |-- Cytoscape.Usage.pdf
|   |   |   |   |-- Medusa.jar
|   |   |   |   |-- sample2-VS-sample1.Cytoscape.txt
|   |   |   |   |-- sample2-VS-sample1.glist
|   |   |   |   |-- sample2-VS-sample1.subnetwork
|   |   |   |   |-- lib
|   |   |   |   |-- network.html
|   |   |   |   `-- network_en.html
|   |   |   |-- Pathway
|   |   |   |   |-- sample2-VS-sample1.path.enrichment.png
|   |   |   |   |-- sample2-VS-sample1.htm
|   |   |   |   |-- sample2-VS-sample1.ko
|   |   |   |   `-- sample2-VS-sample1.path
|   |   |   `-- TranscriptionFactor
|   |   |       `-- sample2-VS-sample1.TFCodingGene.xls
|   |   `-- GenePCA
|   |       |-- PCA.exp.xls.3D.pdf
|   |       |-- PCA.exp.xls.3D.png
|   |       |-- PCA.exp.xls.pca_figure-0.png
|   |       |-- PCA.exp.xls.pca_figure-1.png
|   |       |-- PCA.exp.xls.pca_figure-2.png
|   |       |-- PCA.exp.xls.pca_figure-3.png
|   |       |-- PCA.exp.xls.pca_figure.pdf
|   |       |-- PCA.exp.xls.scatter.pdf
|   |       `-- PCA.exp.xls.scatter.png
|   `-- 4.StructureAnalysis	[ All result files that related to structure analysis of each sample are stored in this folder. ]
|       |-- AlternativeSplicing
|       |   |-- sample1.A3SS.xls
|       |   |-- sample1.A5SS.xls
|       |   |-- sample1.RetainedIntron.xls
|       |   |-- sample1.SkippedExon.xls
|       |   |-- sample1.png
|       |   `-- sample1.svg
|       |-- ExtendGene
|       |   `-- sample1_ExtendGene.xls
|       |-- GeneFusion
|       |   |-- sample1.GeneFusion.png
|       |   |-- sample1.final.Fusion.specific.for.genes
|       |   |-- sample1.final.Fusion.specific.for.trans
|       |   |-- sample1.final.Junc_reads
|       |   |-- sample1.final.Span_reads
|       |   1-- sample1.fusions_expression
|       |-- Indel
|       |   `-- sample1.indel.vcf
|       |-- NovelTU
|       |   |-- sample1.Novel_TU.fa
|       |   |-- sample1.Novel_TU.xls
|       |   |-- sample1.check
|       |   `-- novelTranscript.png
|       |-- RNAedit
|       |   |-- sample1.edit.stat.pdf
|       |   |-- sample1.edit.stat.png
|       |   |-- sample1.edit.stat.xls
|       |   `-- sample1.edit.xls
|       `-- SNP
|           |-- sample1.snp.AnnotationTable.xls
|           |-- sample1.snp.annot.csv
|           |-- sample1.snp.vcf.xls
|           |-- Snp_Distr_R.pdf
|           `-- Snp_Distr_R.png
|-- Pages	[ Other files related to html report are stored in this folder ]
|-- index.html	[ index webpage of report in Chinese ]
|-- index_en.html	[ index webpage of report in English ]
|-- report.pdf		[ PDF report in Chinese ]
`-- report_en.pdf	[ PDF report in English ]