Guideline

Guidelines will continued to be released and updated. For more questions, please contact us directly by email or telephone.
scRNA-Seq guideline
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RNA-Seq-DEG guideline
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WES/WGS-somatic guideline
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Software Information

The table below lists all software tools and their versions used in ViPMAP pipelines for analyses.
Tools Omics Pipeline Version Link
ABSOLUTE DNA-Seq Somatic-CNV 1.0.6 https://www.genepattern.org/analyzing-absolute-data
Annovar DNA-Seq Germline 2020-06-08 00:46:07 -0400 https://annovar.openbioinformatics.org/en/latest/
Annovar DNA-Seq Somatic-SNV 2020-06-08 00:46:07 -0400 https://annovar.openbioinformatics.org/en/latest/
Bismark Methylation WGBS 0.23.0 https://felixkrueger.github.io/Bismark/
Bowtie2 ChIP-Seq/ATAC-Seq 2.3.5 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Bowtie2 Methylation WGBS 2.4.2 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
BWA DNA-Seq Germline 0.7.17-r1188 https://bio-bwa.sourceforge.net/
BWA DNA-Seq Somatic-CNV 0.7.17-r1188 https://bio-bwa.sourceforge.net/
BWA DNA-Seq Somatic-SNV 0.7.17-r1188 https://bio-bwa.sourceforge.net/
BWA RNA-Seq CircleRNA 0.7.15-r1140 https://bio-bwa.sourceforge.net/
Cell Ranger scRNA-Seq 10X 3.0.1 https://www.10xgenomics.com/support
Cellassign scRNA-Seq 10X 0.99.16 https://github.com/Irrationone/cellassign
ChAMP Methylation BeadChip 2.24.0 https://bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html
ChIPseeker ChIP-Seq/ATAC-Seq v1.18.0 https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
ChIPseeker Methylation WGBS 1.32.1 https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
CIRCexplorer2 RNA-Seq CircleRNA 2.3.6 https://circexplorer2.readthedocs.io/en/latest/
CIRI RNA-Seq CircleRNA 2.0.6 https://sourceforge.net/projects/ciri/files/CIRI2/
Deeptools ChIP-Seq/ATAC-Seq 3.3.0 https://test-argparse-readoc.readthedocs.io/en/latest/
DESeq2 RNA-Seq DEG 1.24.0 https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
DSS Methylation WGBS 2.44.0 https://bioconductor.org/packages/release/bioc/vignettes/DSS/inst/doc/DSS.html
featureCounts RNA-Seq DEG 1.6.3 https://subread.sourceforge.net/featureCounts.html
featureCounts RNA-Seq SmartSeq 1.6.3 https://subread.sourceforge.net/featureCounts.html
GATK4:CNV DNA-Seq Somatic-CNV 4.1.8.1 4.1.9.0 4.2.2.0 https://gatk.broadinstitute.org/hc/en-us
GATK4:FilterVariants DNA-Seq Somatic-SNV 4.1.8.1 https://gatk.broadinstitute.org/hc/en-us
GATK4:Mutect2 DNA-Seq Somatic-SNV 4.1.8.1 https://gatk.broadinstitute.org/hc/en-us
GATK4:HaplotypeCaller DNA-Seq Germline 4.1.8.1 https://gatk.broadinstitute.org/hc/en-us
HISAT2 RNA-Seq DEG 2.1.0 http://daehwankimlab.github.io/hisat2/manual/
HOMER ChIP-Seq/ATAC-Seq 4.9.1 http://homer.ucsd.edu/homer/index.html
HTSeq RNA-Seq DEG 0.9.1 https://htseq.readthedocs.io/en/master/htseqcount.html
MACS14/2 ChIP-Seq/ATAC-Seq 1.4.2 2.1.1.20160309 https://github.com/macs3-project/MACS
MAFTOOLS DNA-Seq Somatic-SNV 2.8.0 https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html
MapSplice RNA-Seq ASE https://github.com/LiuBioinfo/MapSplice
sambamba:MarkerDuplicates ChIP-Seq/ATAC-Seq 0.8.0 http://lomereiter.github.io/sambamba/index.html
MaxQuant Proteomics 2.0.1.0 http://coxdocs.org/doku.php?id=maxquant:start
Miso RNA-Seq ASE https://miso.readthedocs.io/en/fastmiso/
MutsigCV DNA-Seq Somatic-SNV 1.41 https://www.genepattern.org/modules/docs/MutSigCV
NGSQC Toolkit RNA-Seq ASE 2.3.3 https://github.com/mjain-lab/NGSQCToolkit
NGSQC Toolkit RNA-Seq CircleRNA 2.3.3 https://github.com/mjain-lab/NGSQCToolkit
NGSQC Toolkit RNA-Seq DEG 2.3.3 https://github.com/mjain-lab/NGSQCToolkit
Paean RNA-Seq ASE-GPU https://github.com/Bio-Acc/Paean
rMATs RNA-Seq ASE v4.0.3beta https://rnaseq-mats.sourceforge.io/
RSEM RNA-Seq DEG 1.3.1 https://github.com/deweylab/RSEM
Seurat scRNA-Seq 10X 2.3.4 https://satijalab.org/seurat/
Space Ranger stRNA-Seq 10X 1.3.0 https://www.10xgenomics.com/support
Seurat stRNA-Seq 10X 3.2.3 https://satijalab.org/seurat/
STAR RNA-Seq ASE 2.7.2b https://github.com/alexdobin/STAR
STAR RNA-Seq CircleRNA 2.7.2b https://github.com/alexdobin/STAR
STAR RNA-Seq DEG 2.7.2b https://github.com/alexdobin/STAR
STAR RNA-Seq SmartSeq 2.7.2b https://github.com/alexdobin/STAR
trim_galore ChIP-Seq/ATAC-Seq 0.6.3 https://github.com/FelixKrueger/TrimGalore
Trimmomatic DNA-Seq Germline 0.39 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic DNA-Seq Somatic-CNV 0.39 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic DNA-Seq Somatic-SNV 0.39 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic Methylation WGBS 0.39 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic RNA-Seq ASE 0.36 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic RNA-Seq CircleRNA 0.36 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic RNA-Seq DEG 0.36 http://www.usadellab.org/cms/?page=trimmomatic
Trimmomatic RNA-Seq SmartSeq 0.36 http://www.usadellab.org/cms/?page=trimmomatic
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