Docs Resolwe Bio Process catalog Processes by category Processes by category¶ Atac-seq¶ ATAC-Seq ATAC-Seq (Beta) Align¶ Bowtie (Dicty) Bowtie2 BWA MEM BWA SW BWA ALN BWA MEM2 HISAT2 STAR Bam processing¶ Annotate novel splice junctions (regtools) Bamliquidator Bamplot alignmentSieve Bamclipper MarkDuplicates Bedtools bamtobed Calculate coverage (bamCoverage) Chip-seq¶ MACS 1.4 Batch peak calling (MACS2) ChIP-seq (MACS2-ROSE2) Pre-peak call QC ChipQC MACS 2.0 ROSE2 Differential expression¶ Cuffdiff 2.2 DESeq2 edgeR Enrichment and clustering¶ Find similar genes Hierarchical clustering of time courses Principal component analysis (PCA) Fastq processing¶ Cutadapt (single-end) Cutadapt (paired-end) Trimmomatic (single-end) Trimmomatic (paired-end) BBDuk (single-end) BBDuk (paired-end) Cutadapt (3’ mRNA-seq, single-end) Cutadapt (Corall RNA-Seq, single-end) Cutadapt (Corall RNA-Seq, paired-end) Trim Galore (paired-end) Merge FASTQ (single-end) Merge FASTQ (paired-end) Subsample FASTQ (single-end) Subsample FASTQ (paired-end) UMI-tools dedup Gatk¶ BaseQualityScoreRecalibrator RNA-seq variant calling preprocess GATK SplitNCigarReads GATK GenomicsDBImport GATK HaplotypeCaller (GVCF) GATK4 (HaplotypeCaller) GATK MergeVcfs GATK SelectVariants (multi-sample) GATK SelectVariants (single-sample) GATK VariantFiltration (multi-sample) GATK VariantFiltration (single-sample) GATK refine variants GATK GenotypeGVCFs GATK VariantsToTable GATK filter variants (VQSR) Gene fusions¶ Arriba Genome index¶ Bowtie2 genome index Bowtie genome index BWA genome index BWA-MEM2 genome index HISAT2 genome index STAR genome index Import¶ GFF3 file GTF file BED file BAM file BAM file and index Cuffquant results Differential Expression (table) GAF file OBO file Mappability info VCF file BEDPE file BaseSpace file BWA-MEM2 index files Ensembl-VEP cache directory Gene set Gene set (create) Metadata table (one-to-one) Metadata table IDAT file ML-ready expression FASTA file FASTQ file (single-end) FASTQ file (paired-end) Convert files to reads (single-end) Convert files to reads (paired-end) SRA data SRA data (single-end) SRA data (paired-end) Upload microarray expression (unmapped) GEO import Other¶ Archive samples Convert GFF3 to GTF GTF to BED Picard¶ Picard AlignmentSummary Picard InsertSizeMetrics Picard CollectRrbsMetrics Picard WGS Metrics Pipeline¶ Chemical Mutagenesis MACS2 - ROSE2 MACS2 Subsample FASTQ and BWA Aln (single-end) Subsample FASTQ and BWA Aln (paired-end) Cutadapt - STAR - StringTie (Corall, single-end) Cutadapt - STAR - StringTie (Corall, paired-end) RNA-Seq (Cuffquant) miRNA pipeline Whole exome sequencing (WES) analysis WGBS (single-end) WGBS (paired-end) WGS (paired-end) analysis BBDuk - Salmon - QC STAR-based gene quantification workflow BBDuk - STAR - featureCounts - QC Cut & Run workflow Gene Fusion Calling with Arriba QuantSeq workflow RNA-seq Variant Calling Workflow WGS analysis (GVCF) Qc¶ Spike-ins quality control MultiQC QoRTs QC RNA-SeQC Quantify¶ Cufflinks 2.2 Cuffnorm Cuffquant 2.2 Dictyostelium expressions Mappability Expression matrix Salmon Index Expression aggregator Detect library strandedness Samtools¶ Samtools fastq (paired-end) Samtools bedcov Samtools coverage (multi-sample) Samtools coverage (single-sample) Samtools depth (single-sample) Samtools mpileup (single-sample) Samtools view Samtools idxstats Test¶ Abstract alignment process Abstract annotation process Abstract differential expression process Abstract expression process Abstract bed process Test basic fields Test disabled inputs Test hidden inputs Test select controler Test sleep progress Vep¶ Ensembl Variant Effect Predictor Wgbs¶ HMR methcounts WALT Bisulfite conversion rate WALT genome index Wgs¶ Variant filtering (CheMut) snpEff (General variant annotation) (multi-sample) snpEff (General variant annotation) (single-sample) Variant calling (CheMut) WGS preprocess data with bwa-mem2 Xenograft processing¶ Xengsort index Xengsort classify Uncategorized¶ Map microarray probes