Question: ATACseqQC: a few questions
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gravatar for david.mckinnon
9 months ago by
david.mckinnon0 wrote:

I have a few questions related to this package, which has generally worked well and is an easy way to perform preliminary analysis of ATAC-seq data.

1. I do not understand the output from the  cumulativePercentage  function described in the vignette. The plot shown in the vignette is very different from what we saw using our data. Otherwise our data look similar to the data described in the paper (see image below). 

2. Is it possible to get a Transcription Start Site (TSS) Enrichment Score from your program? This measure is described here: https://www.encodeproject.org/data-standards/terms/#enrichment

Ultimately, I would like to submit our data to Encode so it would be useful to check that it passes their criteria.

atacseqqc • 227 views
ADD COMMENTlink modified 9 months ago by Julie Zhu4.0k • written 9 months ago by david.mckinnon0
Answer: ATACseqQC: a few questions
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gravatar for Julie Zhu
9 months ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
David, Thanks for the feedback! Regarding the output from cumulativePercentage, you are unlikely to get a plot that looks exactly the same as the one shown in the vignette. The further away from the y = x line the curve is, the higher the signal noise ratio is. We will add the Transcription Start Site (TSS) Enrichment Score later ( https://www.encodeproject.org/data-standards/terms/#enrichment) Best regards, Julie ________________________________
ADD COMMENTlink modified 9 months ago • written 9 months ago by Julie Zhu4.0k
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