Why Diffbind function dba.peakset gives 1
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galib36 ▴ 10
@galib36-9138
Last seen 6.2 years ago
United Kingdom

Hello Rory,

I am using diffbind to extract the raw counts for my PEAKS. I used the function

myData.RawCount <- dba.count(myData, score=DBA_SCORE_READS)

myData.RawCount.value <- dba.peakset(myData.RawCount, bRetrieve=TRUE, writeFile="../RawReads.txt")

I am using it for Single-cell ATAC seq analysis. But when I open the file, I see that the file have no Zeros. Its only 1 and value above 1. But for peaks that does not have any count, shouldn't it be 0? Why there are 1 instead of 0s.

When I use, the bedtools multicov for counts, it gives me lots of zeros (as I would expect in single-cell)

 

Thank you.

 

Best Regards,

Syed

diffbind • 1.1k views
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Rory Stark ★ 5.1k
@rory-stark-5741
Last seen 9 weeks ago
Cambridge, UK
Hello Syed- DiffBind sets all read counts to a minimum value of 1. For purposes of calculating differential binding, differences in sampling at the single read level should not alter the results. Cheers- Rory Sent from my phone On 15 Apr 2016, at 07:56, galib36 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User galib36<https: support.bioconductor.org="" u="" 9138=""/> wrote Question: Why Diffbind function dba.peakset gives 1<https: support.bioconductor.org="" p="" 80888=""/>: Hello Rory, I am using diffbind to extract the raw counts for my PEAKS. I used the function myData.RawCount <- dba.count(myData, score=DBA_SCORE_READS) myData.RawCount.value <- dba.peakset(myData.RawCount, bRetrieve=TRUE, writeFile="../RawReads.txt") I am using it for Single-cell ATAC seq analysis. But when I open the file, I see that the file have no Zeros. Its only 1 and value above 1. But for peaks that does not have any count, shouldn't it be 0? Why there are 1 instead of 0s. When I use, the bedtools multicov for counts, it gives me lots of zeros (as I would expect in single-cell) Thank you. Best Regards, Syed ________________________________ Post tags: diffbind You may reply via email or visit Why Diffbind function dba.peakset gives 1
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Asking the following question just for a bit of more clarification,

I have two sets of single cells, each composed of 96 cells. When using bedtools multimap, I combine the peakset from all these 192 cells and then count the overlapping peaks to have the count for each cell. I was wondering, is this the same approach that Diffbind takes. Because I found some dissimilarity in the count of Diffbind and bedtools multicov.

 

Thank you again.

Best Regards,

Syed

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galib36 ▴ 10
@galib36-9138
Last seen 6.2 years ago
United Kingdom

Thank you for the Clarification

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