ChIPQCreport Total number of duplicates differs from multiqc/fastqc & RelCC is Inf
1
0
Entering edit mode
ZheFrench ▴ 60
@zhefrench-11689
Last seen 11 weeks 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 • 1.9k views
ADD COMMENT
0
Entering edit mode
@thomas-carroll-7019
Last seen 2.0 years 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

 

 

 

ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

tom

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 738 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6