Question: ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
0
gravatar for ZheFrench
22 months ago by
ZheFrench10
ZheFrench10 wrote:

Total number of duplicates in ChIPQC differs from multiqc ? I check all chromosomes not just one...

In fact 0 duplicates are found with ChIPQC ? How ChiPQC retrieve duplicate ? How can it be explain ? 

Also RelCC is Inf for one of my sample , what does it mean ?

 

chipqc chipqcreport • 401 views
ADD COMMENTlink modified 22 months ago by Thomas Carroll400 • written 22 months ago by ZheFrench10
Answer: ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is I
0
gravatar for Thomas Carroll
22 months ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:

Hi,

Chipqc looks for SAM flags marking reads as duplicates as provided by Picard's markdupicates tool.

 

So it will report only if reads have been marked so then I suspect  duplicated rate is zero because of this here

We will move to  some of the code  for duplicate counting without marking in the very near future

A negative score often suggests a low enrichment, could you share the figure with me privately and I can take a look?

Best 

Tom

 

 

 

ADD COMMENTlink written 22 months ago by Thomas Carroll400

I send you a message on your email with questions regarding the results I get with ChIPQC on my data.

Thanks for you help. 

ADD REPLYlink written 21 months ago by ZheFrench10

Okay great, could you accept the answer here for now?  I'll reply to your other message there

tom

ADD REPLYlink written 21 months ago by Thomas Carroll400

Hi Tom, 

Could you post the potential reason for why dup% is 0? My input files are BAM files. Both QC report from before and after I performed the deduplication using fastx_collapser from FASTX-Toolkit showed the same results. 

Thanks!

ADD REPLYlink written 5 months ago by molly_the_minotaur20
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