User: lindahove

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lindahove10
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New User
Location:
Denmark
Last seen:
3 years, 11 months ago
Joined:
4 years, 2 months ago
Email:
l********@gmail.com

Posts by lindahove

<prev • 6 results • page 1 of 1 • next >
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Error in ChIPQC
...   Hi, I have made a sample sheet on 49 samples containing both histone marks, pol2 and transcription factors (TF). Its sample sheet I was able to read with ChIPQC() function without any errors. As I was recommended to handle broad marks  separately I split the data sheet. However now I get the fo ...
chipseq chipq written 4.1 years ago by lindahove10 • updated 4.1 years ago by Valerie Obenchain6.7k
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Answer: A: ChIPQC and broadPeak input
... Hi Tom, Thanks for your help - all the plots are working now. I have a question regarding the peak profiles of my controls. They all seems very much enriched ... also more than many of my ip samples  - however these "enrichments" is not spotted in the control pileup files from macs2 when inspectin ...
written 4.2 years ago by lindahove10
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Answer: A: ChIPQC and broadPeak input
... Have done (-: Thanks. I only think That is a problem with the plotCC, no also the plotPeakProfile Cheers,   ...
written 4.2 years ago by lindahove10
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Comment: C: ChIPQC and broadPeak input
... Hi Thomas - Thanks ! I will share a google drive folder containing the Rdata objects. However what email should I share to? It should be noted that it seems as if the data is low-quality )-: Cheers, Linda ...
written 4.2 years ago by lindahove10
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Answer: A: ChIPQC and broadPeak input
... Thanks for your reply! I have called peaks with MACS2 - and are now trying to figure out how obtain the QC metrics for h3k4me3, h3k27me3 and pol2 domains. I just keep getting the following error:    > ChIPQCreport(samples) Saving 7 x 7 in image Error in `$<-.data.frame`(`*tmp*`, "SCALE_X" ...
written 4.2 years ago by lindahove10
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ChIPQC and broadPeak input
... Hi All, New to this forum - so please correct me if this Q is misplaced. Is it possible to do ChIP-seq QC on broad peaks (diffuse histone marks and pol2) with ChIPQC? Maybe by using the PeakCaller="macs". Found no documentation regarding this Kind regards, Linda ...
chipseq chipqc chip-seq written 4.2 years ago by lindahove10

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For ChIPQC and broadPeak input

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