table in multiqc report showing how reads change at various steps

[kelly-sovacool]

Description of feature

similar to:

columns:

Nreads_raw .. in raw fastqs
Nreads_trimmed ... after trimming
Percentage after trimming w.r.t Nreads_raw
Nreads_mapped ... after mapping
Percentage mapped out of Nreads_trimmed and NOT Nreads_raw
Nreads_Q5DD ... after Q5DD filtering
Percentage Q5DD again w.r.t Nreads_trimmed
Nreads_peaks ... number of reads in peaks  
Percentage in peaks ... w.r.t Nreads_Q5DD ... NOT Nreads_trimmed or Nreads_mapped or Nreads_raw ..  This is the same as "FRiP"

[kopardev]

Here is another example of data that needs to be collated in inserted into a report ... possible custome MultiQC itself:

[kopardev]

@kelly-sovacool are these metrics calculated currently?

[kelly-sovacool]

Some of them are and are already included in the multiqc report, but they aren't all included in the same table

[kopardev]

@kelly-sovacool , I found what I needed .. but we need to revisit and revamp the MultiQC report at some point so it become more comprehensive. For example: it is missing:

• No. of peaks per replicate
• No. of peaks per sample (consensus peaks)
• Peak annotations from chipseeker