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:
2 days ago
Joined:
3 years ago
Email:
t************@gmail.com

Posts by Thomas Carroll

<prev • 81 results • page 1 of 9 • next >
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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 11 days 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 15 days 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 16 days 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 7 weeks 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 8 weeks 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 12 weeks 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 12 weeks 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 12 weeks 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 12 weeks ago by Thomas Carroll390
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Answer: A: ChiPQC run time error
... hi, Could you provide the session information by running sessionInfo() function?   > sessionInfo() best, tom ...
written 4 months ago by Thomas Carroll390

Latest awards to Thomas Carroll

Scholar 5 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 5 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 7 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 21 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 21 months ago, created an answer that has been accepted. For A: ChIPQC and broadPeak input
Scholar 21 months ago, created an answer that has been accepted. For A: shiftApply verbosity (in ChIPQC)
Scholar 21 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Scholar 21 months ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.1 years ago, created an answer that has been accepted. For A: ChIPQC v1.4 fails uninformatively where version 1.2 works fine
Scholar 2.6 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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