ammawla/encode-toolkit
7 subagents
Subagent
atacseq-pipelineExecute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2chipseq-pipelineExecute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDRcutandrun-pipelineExecute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalizationdnaseseq-pipelineExecute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAChic-pipelineExecute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPSrnaseq-pipelineExecute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallistowgbs-pipelineExecute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel