Docs Resolwe Bio Index Index A | B | C | D | E | F | G | H | I | M | O | P | Q | R | S | T | U | V | W | X A Abstract alignment process Abstract annotation process Abstract bed process Abstract differential expression process Abstract expression process alignmentSieve Annotate novel splice junctions (regtools) Archive samples Arriba ATAC-Seq (Beta) B BAM file BAM file and index Bamclipper Bamliquidator Bamplot BaseQualityScoreRecalibrator BaseSpace file Batch peak calling (MACS2) BBDuk (paired-end) (single-end) BBDuk - Salmon - QC BBDuk - STAR - featureCounts - QC BED file BEDPE file Bedtools bamtobed Bisulfite conversion rate Bowtie (Dicty) Bowtie genome index Bowtie2 Bowtie2 genome index BWA ALN BWA genome index BWA MEM BWA MEM2 BWA SW BWA-MEM2 genome index BWA-MEM2 index files C Calculate coverage (bamCoverage) Chemical Mutagenesis ChIP-seq (MACS2-ROSE2) ChipQC Convert files to reads (paired-end) (single-end) Convert GFF3 to GTF Cuffdiff 2.2 Cufflinks 2.2 Cuffnorm Cuffquant 2.2 Cuffquant results Cut & Run workflow Cutadapt (3' mRNA-seq, single-end) (Corall RNA-Seq, paired-end) (Corall RNA-Seq, single-end) (paired-end) (single-end) Cutadapt - STAR - StringTie (Corall, paired-end) (Corall, single-end) D DESeq2 Detect library strandedness Dictyostelium expressions Differential Expression (table) E edgeR Ensembl Variant Effect Predictor Ensembl-VEP cache directory Expression aggregator Expression matrix F FASTA file FASTQ file (paired-end) (single-end) Find similar genes G GAF file GATK filter variants (VQSR) GATK GenomicsDBImport GATK GenotypeGVCFs GATK HaplotypeCaller (GVCF) GATK MergeVcfs GATK refine variants GATK SelectVariants (multi-sample) (single-sample) GATK SplitNCigarReads GATK VariantFiltration (multi-sample) (single-sample) GATK VariantsToTable GATK4 (HaplotypeCaller) Gene Fusion Calling with Arriba Gene set (create) GEO import GFF3 file GTF file GTF to BED H Hierarchical clustering of time courses HISAT2 HISAT2 genome index HMR I IDAT file M MACS 1.4 MACS 2.0 MACS2 MACS2 - ROSE2 Map microarray probes Mappability Mappability info MarkDuplicates Merge FASTQ (paired-end) (single-end) Metadata table (one-to-one) methcounts miRNA pipeline ML-ready expression MultiQC O OBO file P Picard AlignmentSummary Picard CollectRrbsMetrics Picard InsertSizeMetrics Picard WGS Metrics Pre-peak call QC Principal component analysis (PCA) Q QoRTs QC QuantSeq workflow R RNA-Seq (Cuffquant) RNA-seq variant calling preprocess RNA-seq Variant Calling Workflow RNA-SeQC ROSE2 S Salmon Index Samtools bedcov Samtools coverage (multi-sample) (single-sample) Samtools depth (single-sample) Samtools fastq (paired-end) Samtools idxstats Samtools mpileup (single-sample) Samtools view snpEff (General variant annotation) (multi-sample) (single-sample) Spike-ins quality control SRA data (paired-end) (single-end) STAR STAR genome index STAR-based gene quantification workflow Subsample FASTQ (paired-end) (single-end) Subsample FASTQ and BWA Aln (paired-end) (single-end) T Test basic fields Test disabled inputs Test hidden inputs Test select controler Test sleep progress Trim Galore (paired-end) Trimmomatic (paired-end) (single-end) U UMI-tools dedup Upload microarray expression (unmapped) V Variant calling (CheMut) Variant filtering (CheMut) VCF file W WALT WALT genome index WGBS (paired-end) (single-end) WGS (paired-end) analysis WGS analysis (GVCF) WGS preprocess data with bwa-mem2 Whole exome sequencing (WES) analysis Writing processes X Xengsort classify Xengsort index