Assay-Specific Tool Configurations

This page shows which tools are automatically configured for each assay type when using the for_assay() factory method.

Assay Types

RNA

Tools configured: bamnado, deeptools, fastqc, fastqscreen, homer, qualimap, salmon, samtools, star, subread, trimgalore

RNA sequencing - measures gene expression levels

ATAC

Tools configured: bamnado, bowtie2, deeptools, fastqc, fastqscreen, homer, lanceotron, macs, meme, picard, qualimap, samtools, subread, trimgalore

Assay for Transposase-Accessible Chromatin - identifies open chromatin regions

SNP

Tools configured: bcftools, bowtie2, fastqc, fastqscreen, qualimap, samtools, trimgalore

Single Nucleotide Polymorphism analysis - identifies genetic variants

CHIP

Tools configured: bamnado, bowtie2, deeptools, fastqc, fastqscreen, homer, lanceotron, macs, meme, picard, qualimap, samtools, subread, trimgalore

Chromatin Immunoprecipitation sequencing - maps protein-DNA interactions

CUT&TAG

Tools configured: bamnado, bowtie2, deeptools, fastqc, fastqscreen, homer, lanceotron, macs, meme, picard, qualimap, samtools, seacr, subread, trimgalore

METH

Tools configured: bowtie2, fastqc, fastqscreen, methyldackel, picard, qualimap, samtools, trimgalore

DNA methylation analysis - maps methylation patterns

MCC

Tools configured: bamnado, bowtie2, deeptools, fastqc, fastqscreen, lanceotronmcc, qualimap, samtools, trimgalore

CRISPR

Tools configured: bowtie2, cutadapt, fastqc, fastqscreen, mageck, qualimap, qualimap, samtools, subread

CRISPR screening analysis - analyzes guide RNA performance

MULTIOMICS

Tools configured: