Moderator: t.kuilman

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t.kuilman100
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100
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Location:
Netherlands
Website:
https://github.com/Pee...
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 1 month ago
Email:
t********@nki.nl

I am a postdoctoral fellow at the Netherlands Cancer Institute focussing on both biological and bioinformatic approaches to understand cancer drug responses.

Posts by t.kuilman

<prev • 36 results • page 2 of 4 • next >
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Error using countBam (Rsamtools package)
... I have run a very large bam (186 G) file through the countBam function from the Rsamtools package, and got an unexpected error: > library(Rsamtools) > countBam(large.bam.file) Error in value[[3L]](cond) : 'countBam' failed: record: -2023186199 error: 0 file: /home/NFS/research_projec ...
rsamtools countbam written 18 months ago by t.kuilman100
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Comment: C: Preparing CopywriteR output for GISTIC 2.0 analysis
... Thanks for pointing that out, I will adjust the original answer to incorporate your comment. ...
written 21 months ago by t.kuilman100
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Answer: A: Preparing CopywriteR output for GISTIC 2.0 analysis
... GISTIC is probably written for analyzing DNAcopy objects since it requires exactly the output format of DNAcopy objects. The segment.Rdata file contains all the information that you need. By loading this file and accessing the data structure using str(segment.CNA.object), you can see that both the o ...
written 21 months ago by t.kuilman100
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Comment: C: Visualizing CopywriteR's segmentation output in IGV
... Seqlevels are the names of the chromosomes, and none of these are in common. Could it be that you have different chromosome notations (i.e., "chr1" vs "1") in your segment.Rdata file and your GC_mappability.rda file? You can check this by typing segment.CNA.object$output$chrom after loading segment. ...
written 21 months ago by t.kuilman100
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Answer: A: Visualizing CopywriteR's segmentation output in IGV
... Thanks! I wrote a small script for that (see below); I hope this is helpful. I have also written another function (OverviewPlot) to make heatmaps straight from a DNAcopy object. You can find it on our GitHub page. Please let us know if there is anything else we can help you with. ## Load segmented ...
written 21 months ago by t.kuilman100
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Comment: C: Calling amplifications and deletions from CopywriteR output
... Thanks! I put a quick script together for that. For reasons of 'browsability' I feel however that it would be better to start a new post, would you be so kind to do that so that I can reply and share the script in the new post? Thomas ...
written 21 months ago by t.kuilman100
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Comment: C: Multithreading CopywriteR on SLURM cluster
... No, it is not required to set a seed for CopywriteR; on the same system using the same input I always get the same end result (as I said, the minute differences in the output you noted before should be a result of the fact that you run CopywriteR on 2 different systems). I hope this solves the issue ...
written 21 months ago by t.kuilman100
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Comment: C: Multithreading CopywriteR on SLURM cluster
... Ok, to me it seems that CopywriteR runs as it should and that the small differences in the .igv file stem from the internal settings of the system you are using. My first thought on the differences in the output from CGHcall is that they come from differences in the way you run the tool. Could it be ...
written 21 months ago by t.kuilman100
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Comment: C: Multithreading CopywriteR on SLURM cluster
... Ok, I am interested to see whether you will manage to get the parallel analysis using CopywriteR working. As to your question: it should not matter whether you run CopywriteR a number of times on single bams, or on the combined set, as long as the provided controls are the same in both analyses (in ...
written 21 months ago by t.kuilman100
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Comment: C: Calling amplifications and deletions from CopywriteR output
... You could continue from the output of CopywriteR using the log2_read_counts.igv file. An easy way to continue can be found below (courtesy of Oscar Krijgsman who co-developed the tool with me). I hope this gets you on the way. Best, Thomas ### Import data from CopywriteR data<-read.table(file= ...
written 21 months ago by t.kuilman100

Latest awards to t.kuilman

Scholar 22 months ago, created an answer that has been accepted. For A: Copyhelper: Preprocession of mappability
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.

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