cutandrun report elements

[abartlett004]

Present in nf-core multiqc report:

• fastqc metrics, including GC content
• mapping percentages (bowtie2)
• reads passing filters (cutadapt)
• trimmed sequence lengths (cutadapt)
• unique/multimappers (bowtie2)
• alignment metrics and stats (samtools)
• duplication stats (picard markDuplicates)
• all-sample correlation heatmap (deeptools)
• PCA (deeptools)
• fingerpring plot (deeptools)
• peak counts, individual and consensus (macs2/seacr)

Present in Upen's cutandrun QC report:

• total reads
• mapping rate
• mapped reads
• PBC1
• PBC2
• non-redundant fraction
• GC percentage
• peak counts
• fraction of reads in peaks
• all-sample correlation heatmap
• PCA plots 1) faceted by antibody 2) all samples 3) zoomed in

Desired in bcbioR template:

• total reads
• mapping rate
• mapped reads
• peak counts
• ?

[eberdan]

1. PCAs need to be done independently for each antibody.
2. Add peak enrichment vs. peak rank
3. Add overlaps between technical replicates (using findOverlapsOfPeaks)
4. correlation heatmaps are also best per antibody

[eberdan]

FriP, NRF, PBC1 and PBC2 should also be in the bcbioR template

[lpantano]

QC example to follow: chipseq QC https://www.dropbox.com/scl/fi/9lz9i9lsj9lzh21wvtd9q/QC_Chipseq_hbc04729.html?rlkey=o82epbhrij7lhd33hsedkohz7&dl=0