User: Günter Klambauer

Reputation:
490
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Trusted
Location:
Austria
Website:
http://www.bioinf.jku....
Last seen:
1 week, 2 days ago
Joined:
5 years, 6 months ago
Email:
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Posts by Günter Klambauer

<prev • 80 results • page 1 of 8 • next >
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Answer: A: Error with plotting with target sequencing data
... Hello, Thanks for using cn.mops. This error could also be related to the graphics devices. Could you please check if the error persist when you use other graphics devices (e.g. "pdf("tmp.pdf"); plot(resCNMOPS,which=5); dev.off()". If the error persists, please run "traceback()" directly after the e ...
written 9 days ago by Günter Klambauer490
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Great, thanks for the heads-up!! ...
written 9 days ago by Günter Klambauer490
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
... Can you please run "traceback()" directly after the error occurs and post it here? ...
written 15 days ago by Günter Klambauer490
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Seems like the sequence names are "chr19_42791865_42792021_CIC" rather than "chr19", that's why the function does not find any reads. Please check why this happens in your BAM file. ...
written 18 days ago by Günter Klambauer490
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Answer: A: Error when use getSegmentReadCountsFromBAM
... Hi, Can you please run "scanBamHeader" (or similar command) from Rsamtools and check the sequence names in the resulting object? Please let me know the results. Regards, Günter ...
written 23 days ago by Günter Klambauer490
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
... Hello Jieqiong Dai, It is really hard to diagnose the problems but it seems that the "getReadCountsFromBAM" function does not find any reads in your BAM files. Have you tried setting the parameter "mode" to "paired" or "unpaired"? Have you upgraded cn.mops and R to the latest version? Do your BAM f ...
written 4 weeks ago by Günter Klambauer490
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Answer: A: cn.MOPs issue with "Error in if (all(segMedianT == 0))"
... There seems to be some problem with the read counts. Can you check the distributions of read counts (the values in your object "bDR"), such as mean, median, max, number of zeros, NAs? ...
written 8 weeks ago by Günter Klambauer490
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Comment: C: Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
... Hello, For good performance you would need eight high quality samples, but if you only have 2 then you can still try it out -- after all, it is the best thing you can do and the alternative would be to not analyse the data. Note, that the performance estimates that we give in our paper will not hol ...
written 9 weeks ago by Günter Klambauer490
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Answer: A: Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
... Hello, Yes, certainly you can cn.mops for that. You might want to use our newly developed "panelcn.mops" that has been optimized for targeted sequencing data: http://www.bioinf.jku.at/software/panelcnmops/  (Paper, Github, Implementation,...) Regards, Günter   ...
written 9 weeks ago by Günter Klambauer490
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Comment: C: about the runs with cn.mops
... Hello Bogdan, You should go with the CNVs in the slot "cnvs()". The integer copy numbers in the slot "cnvr()" are the average integer copy numbers in the whole region. Since the region is larger than the individual CNVs, in fact the region is a union of all CNVs that occur there, the average copy n ...
written 5 months ago by Günter Klambauer490

Latest awards to Günter Klambauer

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops -- if a chromosome does not have CNV ?
Scholar 8 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops -- if a chromosome does not have CNV ?
Scholar 9 months ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Scholar 9 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.0 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.0 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.1 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.1 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.6 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.6 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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