ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
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ZheFrench ▴ 20
@zhefrench-11689
Last seen 8 days ago
France

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 • 834 views
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@thomas-carroll-7019
Last seen 16 months ago
United States/New York/The Rockefeller …

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

 

 

 

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

Thanks for you help. 

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

tom

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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!

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