User: Thomas Carroll
Thomas Carroll • 390
- 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
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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 Carroll • 390
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... 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 Carroll • 390
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... 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 Carroll • 390
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... 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 Carroll • 390
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...
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 Carroll • 390
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... 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 Carroll • 390
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... 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 Carroll • 390
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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 Carroll • 390
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...
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 Carroll • 390
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... 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 Carroll • 390
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: 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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