Input for chipseq qc and whether it is available in cutandrun output:
1) coldata_fn: yes, use nfcore samplesheet
2) multiqc_data_dir:
multiqc_fastqc.txt: yes, needed for total reads
multiqc_samtools_stats.txt: yes, needed for mapped reads, mapped reads pct
multiqc_phantompeakqualtools.txt: no. needed for nsc, rsc, but cutandrun doesnt run this tool. maybe can calculate another way?
multiqc_frip_score-plot.txt: no. needed for frip, but maybe can calculate another way? confusing that this is absent because nf-core output documentation suggests there should be a FRiP score section in their multiqc report. maybe absent because of processes that we skipped?
multiqc_peak_count-plot.txt: yes, but named multiqc_primary_peakcounts_plot.txt
mqc_picard_deduplication_1.txt: yes, needed to calculate nrf
3) peaks_dir: yes
4) counts_fn: no. there are no deseq2 processes run in this pipeline, nor any other processes that would fragment the genome into bins and calculate counts
Input for chipseq qc and whether it is available in cutandrun output:
1)
coldata_fn: yes, use nfcore samplesheet2)
multiqc_data_dir:multiqc_fastqc.txt: yes, needed for total readsmultiqc_samtools_stats.txt: yes, needed for mapped reads, mapped reads pctmultiqc_phantompeakqualtools.txt: no. needed for nsc, rsc, but cutandrun doesnt run this tool. maybe can calculate another way?multiqc_frip_score-plot.txt: no. needed for frip, but maybe can calculate another way? confusing that this is absent because nf-core output documentation suggests there should be a FRiP score section in their multiqc report. maybe absent because of processes that we skipped?multiqc_peak_count-plot.txt: yes, but named multiqc_primary_peakcounts_plot.txtmqc_picard_deduplication_1.txt: yes, needed to calculate nrf3)
peaks_dir: yes4)
counts_fn: no. there are no deseq2 processes run in this pipeline, nor any other processes that would fragment the genome into bins and calculate counts