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This article mainly introduces the relevant knowledge of "how to use DESeq2". The editor shows you the operation process through an actual case. The operation method is simple, fast and practical. I hope this article "how to use DESeq2" can help you solve the problem.

Deseq_analysis.r differential gene analysis of DESeq2

Usage: $Rscript $scriptdir/deseq_analysis.r-husage: / work/my_stad_immu/scripts/deseq_analysis.r [- h]-I filepath-m filepath-t treatname-- control CONTROL-- case CASE [- f fdr] [- c fc] [- s size] [- an alpha] [- X x.lab] [- Y y.lab] [- T title] [- H height] [- W width] [- o path] [- p prefix] DESeq2 analysis: https://www..com/article/1500optional arguments:-h -- help show this help message and exit-I filepath,-- input filepath input read count file [required]-m filepath,-- metadata filepath metadata file, required-t treatname,-- treatname treatname treat colname in group file, required-- control CONTROL set control group name required-- case CASE set case group name required-f fdr -- fdr fdr set fdr threshold [default 0.05]-- c fc,-- fc fc set fold change threshold [default 2]-s size,-- size size point size [optional, default: 0.7]-an alpha,-- alpha alpha point transparency [0-1] [optional, default: 1]-X x.lab,-- x.lab x.lab the label for x axis [optional Default: log2FC]-Y y.lab,-- y.lab y.lab the label for y axis [optional, default:-log10 (FDR)]-T title,-- title title the label for main title [optional, default: Volcano]-H height,-- height height the height of pic inches [default 5]-W width -- width width the width of pic inches [default 5]-o path,-- outdir path output file directory [default / work/my_stad_immu/05.enrich]-p prefix,-- prefix prefix out file name prefix [default Volcano] parameter description:

-I input the gene expression matrix file, which must be a count expression file:

IDTCGA-B7-A5TK-01A-12R-A36D-31TCGA-BR-7959-01A-11R-2343-13TCGA-IN-8462-01A-11R-2343-13TCGA-BR-A4CR-01A-11R-A24K-31TCGA-CG-4443-01A-01R-1157-13TCGA-KB-A93J-01A-11R-A39E-31TCGA-BR-4371-01A-01R-1157-13TSPAN65951403628343484253720274749TNMD3401018DPM14672433017254370652330944415SCYL31260205770214839241451982C1orf1125239921721400234733958FGR1249112728514856941208CFH12831114355387995457121891795FUCA25896785732085625152775303290GCLC2682550914479323642252652418

-k input gene expression matrix file for fpkm or tpm file for correlation analysis:

IDTCGA-B7-A5TK-01A-12R-A36D-31TCGA-BR-7959-01A-11R-2343-13TCGA-IN-8462-01A-11R-2343-13TCGA-BR-A4CR-01A-11R-A24K-31TCGA-CG-4443-01A-01R-1157-13TSPAN659.6541132.8306440.759639.8413153.37611TNMD0.0847080.09165200.0322110DPM1175.9638132.338593.21574187.7617515.6368SCYL38.32186211.024586.65222211.1736812.80849C1orf1123.9844966.1328321.88009512.16763.741654FGR16.3440811.967395.3508462.2093511.53802

-m metadata file path, grouping information of the sample, the first column must correspond to the sample name of the expression file:

Barcodesubtype.hclustStromalScoreImmuneScoreESTIMATEScoreTumourPurityTCGA-B7-A5TK-01A-12R-A36D-31S11026.0572386.8353412.8920.448276TCGA-BR-7959-01A-11R-2343-13S21130.722729.4021860.1240.638667TCGA-IN-8462-01A-11R-2343-13S2112.2318683.9349796.16670.750581TCGA-BR-A4CR-01A-11R-A24K-31S2-1060.35-766.618-1826.970.943814TCGA-CG-4443-01A-01R-1157-13S2-261.577-258.629-520.2060.8635TCGA pay KBMI A93J- 01A-11R-A39E-31S1-202.2551605.121402.8650.688838TCGA-BR-4371-01A-01R-1157-13S2-828.231711.3379-116.8930.832147TCGA-IN-A6RO-01A-12R-A33Y-31S2-1406.5768.58307-1337.980.917683TCGA-HU-A4H3-01A-21R-A251-31S2-619.208538.7225-80.48540.829171TCGAmura A8MVMAFEN 01AUKEI 11RFEI A36DMAE 31S1113.41272309.6472423.060.572976TCGARAVQFI A91XM01A12RLYA414- 31S2-1845.85-590.017-2435.870.969545TCGA-D7-8575-01A-11R-2343-13S2-206.1121392.7991186.6870.711491TCGA-BR-4257-01A-01R-1131-13S1861.0291676.1482537.1770.559167TCGA-BR-8485-01A-11R-2402-13S1373.09611110.5161483.6120.680198TCGA-BR-4370-01A-01R-1157-13S11300.4951802.3273102.8220.488483

-t subtype.hclust-- case S1-- control S2: specify the name of the metadata grouping column, and the comparison group name in the grouping. If the grouping name has spaces, it should be enclosed in quotation marks: "Stage IA"

-- fdr 0.01-- fc 2 sets the screening conditions for differential genes: significance and multiple of differences

Use examples: Rscript $scriptdir/deseq_analysis.r-I. / 01.TCGA_download/TCGA-STAD_gene_expression_Counts.tsv\-k. / 01.TCGA_download/TCGA-STAD_gene_expression_TPM.tsv-- fdr 0.01m.. / 03.TIME/metadata.group.tsv-t subtype.hclust-- case S1-- control S2-p S1_vs_S2 on "how to use DESeq2" is introduced here. Thank you for your reading. If you want to know more about the industry, you can follow the industry information channel. The editor will update different knowledge points for you every day.

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