Hands-on introduction to NGS RNASeq DE analysis-laptop-file-list
From BITS wiki
[ Main_Page | NGS_data_analysis | Hands-on_introduction_to_NGS_RNASeq_DE_analysis ]
may be updated !
last update, 2015/04/23
RNASeq_DATA
|-- [7.8K] bits_logo_color_150px.png
|-- [4.0K] bowtie2_indexes
| |-- [ 10M] chr22-hg19_ensGene.gtf
| |-- [ 50M] chr22-hg19.fa
| |-- [ 23] chr22-hg19.fa.fai
| |-- [2.4M] chr22-hg19_refGene.gtf
| |-- [916M] hg19.1.bt2
| |-- [684M] hg19.2.bt2
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| |-- [684M] hg19.4.bt2
| |-- [ 10K] hg19.dict
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| |-- [125M] hg19_ensGene.1.bt2
| |-- [ 68M] hg19_ensGene.2.bt2
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| |-- [ 68M] hg19_ensGene.4.bt2
| |-- [305M] hg19_ensGene.fa
| |-- [ 26M] hg19_ensGene.fa.tlst
| |-- [ 16] hg19_ensGene.gff -> hg19_ensGene.gtf
| |-- [459M] hg19_ensGene.gtf
| |-- [125M] hg19_ensGene.rev.1.bt2
| |-- [ 68M] hg19_ensGene.rev.2.bt2
| |-- [ 24] hg19_ensGene.ver
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| |-- [132M] hg19_refGene.fa
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| |-- [ 16] hg19_refGene.gff -> hg19_refGene.gtf
| |-- [117M] hg19_refGene.gtf
| |-- [2.0M] hg19_RefSeq.bed.gz
| |-- [916M] hg19.rev.1.bt2
| |-- [684M] hg19.rev.2.bt2
| `-- [3.1K] make_hg19.sh
|-- [4.0K] Final_results
| |-- [4.0K] bamCorrelate_chr22-all
| | |-- [ 122] bamCorrelate_log.txt
| | |-- [ 657] correlation_matrix.txt
| | `-- [ 85K] correlation_spearman.pdf
| |-- [4.0K] chr22-htseq_counts
| | |-- [ 23K] chr22-chr22_SRR1039509_all_mdup_counts.txt
| | `-- [ 94K] chr22_SRR1039509_all_mdup_errorlog.txt
| |-- [4.0K] chr22_SRR1039509_all_mdup
| | |-- [ 34M] chr22_SRR1039509_all_mdup.bam
| | |-- [ 38K] chr22_SRR1039509_all_mdup.bam.bai
| | `-- [ 53M] chr22_SRR1039509_all_mdup-q.bam
| |-- [4.0K] chr22_SRR1039509_all_mdup_fastq
| | |-- [ 18M] chr22_SRR1039509_all_mdup_fastq_1.fastq.gz
| | `-- [ 18M] chr22_SRR1039509_all_mdup_fastq_2.fastq.gz
| |-- [4.0K] htseq_counts
| | |-- [1.0M] SRR1039508_all_counts.txt
| | |-- [ 13K] SRR1039508_all_errorlog.txt
| | |-- [1.0M] SRR1039508_gtf_counts.txt
| | |-- [ 12K] SRR1039508_gtf_errorlog.txt
| | |-- [1.0M] SRR1039509_all_counts.txt
| | |-- [ 12K] SRR1039509_all_errorlog.txt
| | |-- [1.0M] SRR1039509_gtf_counts.txt
| | |-- [ 11K] SRR1039509_gtf_errorlog.txt
| | |-- [1.0M] SRR1039510_all_counts.txt
| | |-- [ 13K] SRR1039510_all_errorlog.txt
| | |-- [1.0M] SRR1039510_gtf_counts.txt
| | |-- [ 12K] SRR1039510_gtf_errorlog.txt
| | |-- [1.0M] SRR1039511_all_counts.txt
| | |-- [ 12K] SRR1039511_all_errorlog.txt
| | |-- [1.0M] SRR1039511_gtf_counts.txt
| | |-- [ 11K] SRR1039511_gtf_errorlog.txt
| | |-- [1.0M] SRR1039512_all_counts.txt
| | |-- [ 16K] SRR1039512_all_errorlog.txt
| | |-- [1.0M] SRR1039512_gtf_counts.txt
| | |-- [ 14K] SRR1039512_gtf_errorlog.txt
| | |-- [1.0M] SRR1039513_all_counts.txt
| | |-- [9.4K] SRR1039513_all_errorlog.txt
| | |-- [1.0M] SRR1039513_gtf_counts.txt
| | |-- [8.7K] SRR1039513_gtf_errorlog.txt
| | |-- [1.0M] SRR1039514_all_counts.txt
| | |-- [ 22K] SRR1039514_all_errorlog.txt
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| | |-- [ 20K] SRR1039514_gtf_errorlog.txt
| | |-- [1.0M] SRR1039515_all_counts.txt
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| | |-- [ 12K] SRR1039515_gtf_errorlog.txt
| | |-- [1.0M] SRR1039516_all_counts.txt
| | |-- [ 15K] SRR1039516_all_errorlog.txt
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| | |-- [ 14K] SRR1039516_gtf_errorlog.txt
| | |-- [1.0M] SRR1039517_all_counts.txt
| | |-- [ 19K] SRR1039517_all_errorlog.txt
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| | |-- [ 17K] SRR1039517_gtf_errorlog.txt
| | |-- [1.0M] SRR1039518_all_counts.txt
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| | |-- [1.0M] SRR1039518_gtf_counts.txt
| | |-- [ 15K] SRR1039518_gtf_errorlog.txt
| | |-- [1.0M] SRR1039519_all_counts.txt
| | |-- [ 12K] SRR1039519_all_errorlog.txt
| | |-- [1.0M] SRR1039519_gtf_counts.txt
| | |-- [ 11K] SRR1039519_gtf_errorlog.txt
| | |-- [1.0M] SRR1039520_all_counts.txt
| | |-- [ 12K] SRR1039520_all_errorlog.txt
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| | |-- [ 11K] SRR1039520_gtf_errorlog.txt
| | |-- [1.0M] SRR1039521_all_counts.txt
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| | |-- [ 12K] SRR1039521_gtf_errorlog.txt
| | |-- [1.0M] SRR1039522_all_counts.txt
| | |-- [ 16K] SRR1039522_all_errorlog.txt
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| | |-- [ 14K] SRR1039522_gtf_errorlog.txt
| | |-- [1.0M] SRR1039523_all_counts.txt
| | |-- [ 17K] SRR1039523_all_errorlog.txt
| | |-- [1.0M] SRR1039523_gtf_counts.txt
| | `-- [ 16K] SRR1039523_gtf_errorlog.txt
| |-- [4.0K] Qualimap_results
| | |-- [4.0K] chr22-counts
| | | `-- [ 23K] chr22_SRR1039509_all_mdup_counts.txt
| | `-- [4.0K] chr22-reports
| | `-- [4.0K] chr22_SRR1039509_all_mdup
| | |-- [611K] chr22_SRR1039509_all_mdup-Qualimap-bamqc-report.pdf
| | |-- [307K] chr22_SRR1039509_all_mdup-Qualimap-rnaseq-report.pdf
| | |-- [6.7K] genome_results.txt
| | |-- [2.9K] qualimap-bamqc_log.txt
| | `-- [1.1M] qualimap-rnaseq_log.txt
| |-- [4.0K] ref
| | |-- [516K] chr22-hg19_ensGene.bed
| | |-- [7.6M] hg19_Ensembl.bed.gz
| | |-- [ 24M] hg19_ensGene.bed
| | `-- [2.0M] hg19_RefSeq.bed.gz
| |-- [4.0K] RobiNA
| | |-- [5.1M] DESeq1_results-all.csv
| | |-- [5.1M] DESeq1-rev_results-all.csv
| | |-- [3.6M] EdgeR_results-all.csv
| | |-- [2.2M] GSE52778-counts.tsv
| | |-- [6.2K] RobiNA-add_symbol.R
| | |-- [4.0K] RobiNA_Deseq1
| | | |-- [4.0K] detailed_results
| | | | |-- [4.7M] full_table_dex-untr.txt
| | | | `-- [2.2M] RobiNA_Deseq1_raw_countstable.txt
| | | |-- [2.2M] GSE52778-counts.tsv
| | | |-- [4.0K] input
| | | |-- [4.0K] log
| | | | `-- [1.1K] RobiNA_Deseq1.log
| | | |-- [4.0K] plots
| | | | |-- [ 25K] hclust.png
| | | | |-- [ 84K] MAplot_dex-untr.png
| | | | |-- [7.9K] PCAplot.pdf
| | | | |-- [ 34K] PCAplot_.png
| | | | |-- [ 52K] vennDiagram_down.png
| | | | |-- [ 52K] vennDiagram_total.png
| | | | `-- [ 51K] vennDiagram_up.png
| | | |-- [4.0K] qualitychecks
| | | |-- [1.7M] RobiNA_Deseq1_results.txt
| | | |-- [163K] RobiNA_Deseq1_summary.pdf
| | | `-- [4.0K] source
| | | |-- [4.0K] lib
| | | | |-- [3.1K] computeGenomicGCcontentTable.R
| | | | |-- [1.0K] ellipse.R
| | | | |-- [ 489] info.R
| | | | |-- [1.9K] malowess.R
| | | | |-- [ 10K] modifiedAffyCoreTools.R
| | | | |-- [5.0K] plotSigDensities.R
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| | | | |-- [2.6K] robinPlotMDS.dge.R
| | | | `-- [ 11K] robinVennDiagram.R
| | | |-- [ 0] rna_seq.type
| | | |-- [ 416] RobiNA_Deseq1_data.xml
| | | |-- [7.6K] RobiNA_Deseq1_DESEQ_main_analysis.R
| | | `-- [ 509] R.session.info.txt
| | |-- [4.0K] RobiNA_Deseq1rev
| | | |-- [4.0K] detailed_results
| | | | |-- [4.7M] full_table_untr-dex.txt
| | | | `-- [2.2M] RobiNA_DESEQ1rev_raw_countstable.txt
| | | |-- [4.0K] input
| | | |-- [4.0K] log
| | | | `-- [1.2K] RobiNA_DESEQ1rev.log
| | | |-- [4.0K] plots
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| | | | |-- [ 83K] MAplot_untr-dex.png
| | | | |-- [7.9K] PCAplot.pdf
| | | | |-- [ 34K] PCAplot_.png
| | | | |-- [ 52K] vennDiagram_down.png
| | | | |-- [ 52K] vennDiagram_total.png
| | | | `-- [ 51K] vennDiagram_up.png
| | | |-- [4.0K] qualitychecks
| | | |-- [1.7M] RobiNA_DESEQ1rev_results.txt
| | | |-- [163K] RobiNA_DESEQ1rev_summary.pdf
| | | `-- [4.0K] source
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| | | | |-- [3.1K] computeGenomicGCcontentTable.R
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| | | | |-- [ 489] info.R
| | | | |-- [1.9K] malowess.R
| | | | |-- [ 10K] modifiedAffyCoreTools.R
| | | | |-- [5.0K] plotSigDensities.R
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| | | | |-- [2.6K] robinPlotMDS.dge.R
| | | | `-- [ 11K] robinVennDiagram.R
| | | |-- [ 0] rna_seq.type
| | | |-- [ 419] RobiNA_DESEQ1rev_data.xml
| | | |-- [7.6K] RobiNA_DESEQ1rev_DESEQ_main_analysis.R
| | | `-- [ 509] R.session.info.txt
| | `-- [4.0K] RobiNA_EdgeR
| | |-- [4.0K] detailed_results
| | | |-- [3.1M] full_table_dex-untr.txt
| | | |-- [2.2M] RobiNA_raw_countstable.txt
| | | `-- [122K] significant_dex-untr.txt
| | |-- [2.2M] GSE52778-counts.tsv
| | |-- [4.0K] input
| | |-- [4.0K] log
| | | `-- [1.2K] RobiNA.log
| | |-- [4.0K] plots
| | | |-- [ 65K] MAplot_dex-untr.png
| | | |-- [ 35K] MDSplot.png
| | | |-- [ 52K] vennDiagram_down.png
| | | |-- [ 53K] vennDiagram_total.png
| | | `-- [ 50K] vennDiagram_up.png
| | |-- [4.0K] qualitychecks
| | |-- [1.7M] RobiNA_results.txt
| | |-- [161K] RobiNA_summary.pdf
| | `-- [4.0K] source
| | |-- [4.0K] lib
| | | |-- [3.1K] computeGenomicGCcontentTable.R
| | | |-- [1.0K] ellipse.R
| | | |-- [ 489] info.R
| | | |-- [1.9K] malowess.R
| | | |-- [ 10K] modifiedAffyCoreTools.R
| | | |-- [5.0K] plotSigDensities.R
| | | |-- [1.0K] RGbox.R
| | | |-- [2.6K] robinPlotMDS.dge.R
| | | `-- [ 11K] robinVennDiagram.R
| | |-- [ 0] rna_seq.type
| | |-- [ 407] RobiNA_data.xml
| | |-- [6.3K] RobiNA_EDGER_main_analysis.R
| | `-- [ 191] R.session.info.txt
| |-- [4.0K] RSeQC_results
| | |-- [1.6K] RSeQC-SRR1039509_all_mdup.bam_log.txt
| | |-- [ 0] SRR1039509_all_mdup.bam.DupRate_plot.r
| | |-- [3.5K] SRR1039509_all_mdup.bam.geneBodyCoverage.curves.pdf
| | |-- [ 186] SRR1039509_all_mdup.bam.geneBodyCoverage.r
| | |-- [ 303] SRR1039509_all_mdup.bam.geneBodyCoverage.txt
| | |-- [ 307] SRR1039509_all_mdup.bam_inferred.txt
| | |-- [1.2K] SRR1039509_all_mdup.bam_inner_distance.inner_distance_freq.txt
| | |-- [8.2K] SRR1039509_all_mdup.bam_inner_distance.inner_distance_plot.pdf
| | |-- [1.4K] SRR1039509_all_mdup.bam_inner_distance.inner_distance_plot.r
| | |-- [ 53M] SRR1039509_all_mdup.bam_inner_distance.inner_distance.txt
| | |-- [5.5K] SRR1039509_all_mdup.bam.junctionSaturation_plot.pdf
| | |-- [ 876] SRR1039509_all_mdup.bam.junctionSaturation_plot.r
| | |-- [ 0] SRR1039509_all_mdup.bam.pos.DupRate.xls
| | `-- [ 0] SRR1039509_all_mdup.bam.seq.DupRate.xls
| |-- [4.0K] SRP033351-chr22_bam
| | |-- [ 40M] chr22_SRR1039508_all.bam
| | |-- [ 38K] chr22_SRR1039508_all.bam.bai
| | |-- [ 34M] chr22_SRR1039509_all.bam
| | |-- [ 38K] chr22_SRR1039509_all.bam.bai
| | |-- [ 45M] chr22_SRR1039512_all.bam
| | |-- [ 40K] chr22_SRR1039512_all.bam.bai
| | |-- [ 29M] chr22_SRR1039513_all.bam
| | |-- [ 36K] chr22_SRR1039513_all.bam.bai
| | |-- [ 46M] chr22_SRR1039516_all.bam
| | |-- [ 40K] chr22_SRR1039516_all.bam.bai
| | |-- [ 56M] chr22_SRR1039517_all.bam
| | |-- [ 42K] chr22_SRR1039517_all.bam.bai
| | |-- [ 38M] chr22_SRR1039520_all.bam
| | |-- [ 38K] chr22_SRR1039520_all.bam.bai
| | |-- [ 39M] chr22_SRR1039521_all.bam
| | `-- [ 37K] chr22_SRR1039521_all.bam.bai
| |-- [4.0K] SRP033351-chr22_fastq
| | |-- [ 21M] chr22_SRR1039508_1.fastq.gz
| | |-- [ 21M] chr22_SRR1039508_2.fastq.gz
| | |-- [ 18M] chr22_SRR1039509_1.fastq.gz
| | |-- [ 18M] chr22_SRR1039509_2.fastq.gz
| | |-- [ 19M] chr22_SRR1039510_1.fastq.gz
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| | |-- [ 24M] chr22_SRR1039512_1.fastq.gz
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| | |-- [ 15M] chr22_SRR1039513_1.fastq.gz
| | |-- [ 15M] chr22_SRR1039513_2.fastq.gz
| | |-- [ 38M] chr22_SRR1039514_1.fastq.gz
| | |-- [ 38M] chr22_SRR1039514_2.fastq.gz
| | |-- [ 23M] chr22_SRR1039515_1.fastq.gz
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| | |-- [ 24M] chr22_SRR1039516_1.fastq.gz
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| | |-- [ 27M] chr22_SRR1039518_1.fastq.gz
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| | |-- [ 22M] chr22_SRR1039519_1.fastq.gz
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| | |-- [ 20M] chr22_SRR1039520_1.fastq.gz
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| | |-- [ 20M] chr22_SRR1039521_1.fastq.gz
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| | |-- [ 25M] chr22_SRR1039522_1.fastq.gz
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| | |-- [ 27M] chr22_SRR1039523_1.fastq.gz
| | `-- [ 27M] chr22_SRR1039523_2.fastq.gz
| |-- [4.0K] SRR1039509_bam
| | |-- [ 18K] MarkDuplicates_SRR1039509_all_log.txt
| | |-- [ 17K] MarkDuplicates_SRR1039509_gtf_log.txt
| | |-- [2.9G] SRR1039509_all_mdup.bam
| | |-- [2.5K] SRR1039509_all_mdup.txt
| | |-- [2.0G] SRR1039509_gtf_mdup.bam
| | `-- [2.5K] SRR1039509_gtf_mdup.txt
| |-- [4.0K] SRR1039509-chr22_read_qc-Results
| | |-- [ 21K] chr22_SRR1039509_1_boxplot.png
| | |-- [334K] chr22_SRR1039509_1_fastqc.html
| | |-- [393K] chr22_SRR1039509_1_fastqc.zip
| | |-- [6.5K] chr22_SRR1039509_1.fastq.gz_statslineplot.pdf
| | |-- [5.1K] chr22_SRR1039509_1.fastq.gz_stats.txt
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| | |-- [ 21K] chr22_SRR1039509_2_boxplot.png
| | |-- [332K] chr22_SRR1039509_2_fastqc.html
| | |-- [390K] chr22_SRR1039509_2_fastqc.zip
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| | `-- [ 0] error.log
| |-- [4.0K] SRR1039509_fastq
| | |-- [331K] SRR1039509_1_fastqc.html
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| | |-- [363K] SRR1039509_2.fastq.pdf
| | `-- [1.4G] SRR1039509.sra
| |-- [4.0K] SRR1039509_read_qc-Results
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| | |-- [ 21K] SRR1039509_1_boxplot.png
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| | |-- [411K] SRR1039509_1_fastqc.zip
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| | |-- [331K] SRR1039509_2_fastqc.html
| | |-- [412K] SRR1039509_2_fastqc.zip
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| |-- [4.0K] tophat2.0.13_results
| | |-- [4.0K] chr22_SRR1039509_all-mappings
| | | |-- [ 34M] accepted_hits.bam
| | | |-- [ 557] align_summary.txt
| | | |-- [ 24K] deletions.bed
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| | | | |-- [2.5K] juncs_db.log
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63 directories, 494 files
