Index

A

Abstract alignment process Abstract annotation process Abstract bed process Abstract differential expression process Abstract expression process Accel Amplicon Pipeline

Align (BWA) and trim adapters Amplicon report Amplicon table Annotate novel splice junctions (regtools) Archive and make multi-sample report for amplicon data Archive samples ATAC-Seq

B

BAM file BAM file and index Bam split Bamliquidator Bamplot BaseSpace file BBDuk (paired-end) (single-end) BBDuk - Salmon - QC (paired-end) (single-end) BBDuk - STAR - FeatureCounts (3' mRNA-Seq, paired-end) (3' mRNA-Seq, single-end)

BBDuk - STAR - featureCounts - QC (paired-end) (single-end) BBDuk - STAR - HTSeq-count (paired-end) (single-end) BED file BioProcessTestCase (class in resolwe_bio.utils.test) Bowtie (Dicty) Bowtie2 BWA ALN BWA MEM BWA SW

C

Chemical Mutagenesis ChIP-Seq (Gene Score) ChIP-seq (MACS2) (MACS2-ROSE2) ChIP-Seq (Peak Score) Convert files to reads (paired-end) (single-end) Convert GFF3 to GTF coverageBed Cuffdiff 2.2 Cufflinks 2.2 Cuffmerge Cuffnorm Cuffquant 2.2

Cuffquant results Custom master file Cutadapt (Diagenode CATS, paired-end) (Diagenode CATS, single-end) (paired-end) (single-end) Cutadapt - STAR - FeatureCounts (3' mRNA-Seq, single-end) Cutadapt - STAR - FeatureCounts - basic QC (3' mRNA-Seq, single-end) Cutadapt - STAR - HTSeq-count (paired-end) (single-end) Cutadapt - STAR - RSEM (Diagenode CATS, paired-end) (Diagenode CATS, single-end) Cutadapt - STAR - StringTie (Corall, paired-end) (Corall, single-end)

D

DESeq2 Detect library strandedness

Dictyostelium expressions Differential Expression (table)

E

edgeR Expression aggregator Expression data (Cuffnorm) (STAR)

Expression matrix Expression Time Course Expression time course

F

FASTQ file (paired-end) (single-end)

featureCounts

G

GAF file GATK3 (HaplotypeCaller) GATK4 (HaplotypeCaller) Gene expression indices Gene set (create from Venn diagram) (create)

GFF3 file GO Enrichment analysis GTF file

H

Hierarchical clustering of genes Hierarchical clustering of samples HISAT2

HMR HTSeq-count (CPM) (TPM)

I

Indel Realignment and Base Recalibration

K

KBBioProcessTestCase (class in resolwe_bio.utils.test)

L

LoFreq (call)

M

MACS 1.4 MACS 2.0 MACS2 MACS2 - ROSE2

Mappability Mappability info Merge Expressions (ETC) methcounts miRNA pipeline

O

OBO file

P

PCA Picard CollectTargetedPcrMetrics Pre-peakcall QC Prepare GEO - ChIP-Seq Prepare GEO - RNA-Seq prepare_amplicon_master_file() (resolwe_bio.utils.test.BioProcessTestCase method)

prepare_annotation() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_annotation_gff() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_bam() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_expression() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_paired_reads() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_reads() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_ref_seq() (resolwe_bio.utils.test.BioProcessTestCase method)

Q

Quantify shRNA species using bowtie2

R

Reads (QSEQ multiplexed, paired) (QSEQ multiplexed, single) resolwe_bio.utils (module)

resolwe_bio.utils.test (module) RNA-Seq (Cuffquant) RSEM

S

Salmon Index SAM header Secondary hybrid BAM file setUp() (resolwe_bio.utils.test.BioProcessTestCase method) (resolwe_bio.utils.test.KBBioProcessTestCase method) shRNA quantification skipDockerFailure() (in module resolwe_bio.utils.test) skipUnlessLargeFiles() (in module resolwe_bio.utils.test)

Slamdunk analysis (paired-end) snpEff, [1] Spike-ins quality control STAR STAR genome index 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 Trimmomatic (paired-end) (single-end) Trimmomatic - HISAT2 - HTSeq-count (paired-end) (single-end)

U

Upload Picard CollectTargetedPcrMetrics

V

Variant calling (CheMut)

Variant filtering (CheMut) VCF file

W

WALT WGBS (paired-end) (single-end)

WGS (paired-end) analysis Whole exome sequencing (WES) analysis Writing processes