cutandrun report elements - Githubissues

bcbio / bcbioR

R package with well defined templates for most common pipelines

https://bcbio.github.io/bcbioR/

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cutandrun report elements #43

Open abartlett004 opened 1 month ago

abartlett004 commented 1 month ago

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 commented 1 month ago

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

eberdan commented 1 month ago

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

lpantano commented 2 weeks ago

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