<p>I'm running the script <code>run_spp_nodups.R</code> from <a href="https://github.com/crazyhottommy/phantompeakqualtools" rel="nofollow noreferrer"><code>phantompeakqualtools</code></a>. The input is a pair of BED 3+3 ("tagalign") files that are roughly 300M, and I'm using 8 threads. How long would you expect it to take? I am happy to provide other info to the extent that I can manage -- post me a comment!</p>

CC BY-SA 3.0
2018-04-13T22:47:26.797Z
Is there a reason you want to use phantompeakqualtools? It's not exactly commonly used.
Devon Ryan
CC BY-SA 3.0
2018-04-15T20:49:47.133Z
If I were building a pipeline from scratch, I probably wouldn't. I am using it as part of Anshul Kundaje's open-source pipeline.

https://github.com/kundajelab/chipseq_pipeline

I'd rather not go in and start rewiring things on my own if it's running properly -- but it's taking long enough that I suspect that something is off. Hence the question.
eric_kernfeld
CC BY-SA 3.0
2018-04-15T20:50:11.557Z
Is there a specific reason that people avoid it?
eric_kernfeld
CC BY-SA 3.0
2018-04-15T22:10:48.627Z
It's a weird hodge-podge of cryptically written and poorly documented scripts that may or may not give reasonable output. It's basically an artifact of a time when ENCODE was producing a LOT of data and no one had any clue how to reasonably QC all of it. So the NSC/RSC metrics (the main point to phantompeakquals) were created. In hindsight, they're not terribly informative, in part due to being incredibly sensitive to settings. Just do some basic QC and call macs2. The pipeline will do just that anyway.
Devon Ryan
<chip-seq>
How long does it typically take to call peaks via `phantompeakqualtools`?
# How long does it typically take to call peaks via `phantompeakqualtools`?

(Asked by: username_0 on 2018-04-13)

I'm running the script `run_spp_nodups.R` from [`phantompeakqualtools`](https://github.com/crazyhottommy/phantompeakqualtools). The input is a pair of BED 3+3 ("tagalign") files that are roughly 300M, and I'm using 8 threads. How long would you expect it to take? I am happy to provide other info to the extent that I can manage -- post me a comment!

**Tags:** chip-seq
> **Comments:**
> **username_1**: Is there a reason you want to use phantompeakqualtools? It's not exactly commonly used.  
> **username_0**: If I were building a pipeline from scratch, I probably wouldn't. I am using it as part of Anshul Kundaje's open-source pipeline.  https://github.com/kundajelab/chipseq_pipeline  I'd rather not go in and start rewiring things on my own if it's running properly -- but it's taking long enough that I suspect that something is off. Hence the question.  
> **username_0**: Is there a specific reason that people avoid it?  
> **username_1**: It's a weird hodge-podge of cryptically written and poorly documented scripts that may or may not give reasonable output. It's basically an artifact of a time when ENCODE was producing a LOT of data and no one had any clue how to reasonably QC all of it. So the NSC/RSC metrics (the main point to phantompeakquals) were created. In hindsight, they're not terribly informative, in part due to being incredibly sensitive to settings. Just do some basic QC and call macs2. The pipeline will do just that anyway.  

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## 0 answers

