User: Thomas Carroll

gravatar for Thomas Carroll
Reputation:
390
Status:
Trusted
Location:
United Kingdom/London/MRC CSC Imperial College London
Website:
http://mrccsc.github.io/
Last seen:
4 months, 3 weeks ago
Joined:
3 years, 8 months ago
Email:
t************@gmail.com

Posts by Thomas Carroll

<prev • 82 results • page 1 of 9 • next >
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Comment: C: ChiPQC run time error
... I don't think there is anything to do. No session information or any details on file inputs.   ...
written 4 months ago by Thomas Carroll390
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Answer: A: ChIPQC Error in .Call2 NCList object is too deep
... hi Victor, hi Herve, Yes, it looks like on chromosome 2 you have an area over 2 millions reads deep (overlapping reads) which means ChIPQC breaches the limit of 100000 set in the way ChIPQC creates the GNCList object.  I will adopt the change suggested by Herve tonight and it should be in the rele ...
written 8 months ago by Thomas Carroll390
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Answer: A: ChIPQC Error in .Call2 NCList object is too deep
... Okay,  I think I will need to take a look at Bam file to debug. Could you share the Bam file with me by Dropbox or something similar? You can send me link at tc.infomatics@gmail.com and we can post solution here if it is useful to others. Vb, tom   ...
written 8 months ago by Thomas Carroll390
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Answer: A: ChIPQC Error in .Call2 NCList object is too deep
... hi, I can see a few problems here. >* Packages too new for Bioconductor version '3.6' >      Version  LibPath                                                          > ChIPQC "1.15.0" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" > downgrade with biocLite("ChIPQC ...
written 8 months ago by Thomas Carroll390
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Answer: A: Can ChIPQC analyze mandarin duck ChIP-Seq data?
...   hi Gary, ChIPQC should work fine for BAM files aligned to any genome. Since there isn't a prebuilt TxDB package for mandarin duck, the summary of gene signal within genic regions is not immediately supported. To run ChIPQC on a single BAM. ChIPQCsample("MyDuckData.bam") I would recommend runn ...
written 9 months ago by Thomas Carroll390
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Answer: A: Unhelpful Errors Running ChIPQC on Computing Cluster
... hi, I am unable to recreate this error in latest version of ChIPQC (ChIPQC_1.13.2 ). I have used some encode data to make an example with public data. Here is the sample sheet setup.   SampleID Tissue Factor Condition Treatment Replicate    bamReads    ControlID                  bamControl 1    M ...
written 10 months ago by Thomas Carroll390
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Answer: A: Soggi regionPlot function gave error when import bigwig file with "percentOfRe
... hi, I will try and recreate this problem with some local data and get back to you tomorrow. best, tom ...
written 10 months ago by Thomas Carroll390
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Comment: C: ChIPQC failed on chrM
...       hi, The original error looks to do with the way ChIPQC calculates cross coverage. The ChrM may cause some problems here because it is circular. I believe there is a way to check for circular chromosomes so I will look to remove any circular chromosomes while providing a warning for the us ...
written 10 months ago by Thomas Carroll390
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Answer: A: ChIPQC failling when run ChIPQC() over 6 samples
...   hi, Sorry for delay, moved to new post/continent recently. I think this maybe that ChIPQC is looking for all chromosome between chr1991 and chr2992, so from your description this will include chromosomes not in your BAM file. > paste0("chr",1991:2992)    [1] "chr1991" "chr1992" "chr1993" "c ...
written 10 months ago by Thomas Carroll390
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Answer: A: Unhelpful Errors Running ChIPQC on Computing Cluster
... hi, I will try and reproduce with some local data and get back you if I need anymore help or data in debugging. speak soon, tom ...
written 10 months ago by Thomas Carroll390

Latest awards to Thomas Carroll

Scholar 12 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 13 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 13 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 15 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.4 years ago, created an answer that has been accepted. For A: ChIPQC and broadPeak input
Scholar 2.4 years ago, created an answer that has been accepted. For A: shiftApply verbosity (in ChIPQC)
Scholar 2.4 years ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Scholar 2.4 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.4 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.8 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 3.2 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine

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