User: Matthias Lienhard

Reputation:
140
Status:
Trusted
Location:
Max Planck Institute for molecular Genetics, Berlin, Germany
Website:
http://www.molgen.mpg....
Scholar ID:
Google Scholar Page
Last seen:
1 month ago
Joined:
4 years, 4 months ago
Email:
l*******@molgen.mpg.de

Education

  • 2008: Bachelor of Science in Bioinformatics, FU Berlin (Germany)
  • 2011: Master of Science in Bioinformatics, FU Berlin
  • Since 2012: PhD studies at the IMPRS-CBSC supervised by Dr. Ralf Herwig

 

Posts by Matthias Lienhard

<prev • 19 results • page 1 of 2 • next >
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Comment: C: QSEA: Need help on creating ROI for whole genome MeDIPSeq data
... Dear Vivek, retrieving annotation is not within the scope of qsea. You are right, for the tutorial I provide a example for the analyzed chromosomes. You can create these objects yourself, by downloading tables from the UCSC table browser, import them in R (e.g. by read.table()) and then create a GR ...
written 8 weeks ago by Matthias Lienhard140
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Comment: C: QSEA Error while loading the bam files
... Hi Vivek, I am happy to hear that it works now. Can you please "accept" the answer if your issue is fully solved? Best, Matthias ...
written 8 weeks ago by Matthias Lienhard140
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Answer: A: QSEA: Need help on creating ROI for whole genome MeDIPSeq data
... Hi Vivek, in qsea, makeTable offers two possibilities to look at regions of interest (ROIs): The "ROIs" parameter takes a GRange object selects all windows that overlap with these Genomic Ranges. Windows overlapping with more than one ROI are represented several times. The "annotation" parameter ...
written 8 weeks ago by Matthias Lienhard140
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Answer: A: QSEA: Error while addLibraryFactors
... Hi Vivek, I did some tests and could reproduce your error, if I don't add the CpG density to the qsea set before calling addLibraryFactors - I guess this was also the case for you. For now I recommend calling addPatternDensity before addLibraryFactors. If this does not help, please let me know. I ...
written 8 weeks ago by Matthias Lienhard140
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Answer: A: QSEA Error while loading the bam files
... Hi geekyvt, I could not reproduce the error. As long as the two bam files are present, your script does not produce an error for me. Can you please confirm that you are using the latest version of bioconductor, along with the corresponding version of R? Also, in the ceateQseaSet step, only the pres ...
written 8 weeks ago by Matthias Lienhard140
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Comment: C: CNV parameter not working - MEDIPS
... Unfortunately, MEDIPS.getAnnotation does not fetch gene names, and the function cannot be configured, such that it does fetch them. You could either modify the function, or match the ids and change the resulting output tables manually. ...
written 11 months ago by Matthias Lienhard140
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Comment: C: CNV parameter not working - MEDIPS
... Hi Anupriya, within MEDIPS, the calculation of CNV works by comparing the local coverage of the input sample(s)  that contain CNVs (ISet2) to the control input sample(s) (ISet1). Therefore it is required to specify both sets. However, probably the read coverage is not sufficient to run the CNV det ...
written 11 months ago by Matthias Lienhard140
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Answer: A: CNV parameter not working - MEDIPS
... Hi Anupriya Verma, MEDIPS.createSet calculates CNVs based on the window size selected for the primary MeDIP seq analysis. In most cases, the input coverage is not sufficient for CNV detection at this resolution. Maybe, that this somehow leads to the error message you got. The suggested way would be ...
written 11 months ago by Matthias Lienhard140
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Answer: A: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
... Hi Justin, I used two perl script to summarize the TCGA data into genome wide bins: 1) SummarizeTables.pl combines several sample files in a single table. 2) summarize_bs_in_bins.pl sumerizes bisulfite values in genome wide bins of fixed size by computing the average % methylation values. I prov ...
written 12 months ago by Matthias Lienhard140
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Comment: C: Alternative methylation contexts with MEDIPS?
... Hi Chris, maybe I wasn't clear, what I ment was the following behavior of matchPattern, when setting fixed=F >library(BSgenome.Hsapiens.UCSC.hg19) >library(Biostrings) >chr_seq=getBSgenome("BSgenome.Hsapiens.UCSC.hg19")[["chr1"]] >chr_seq   249250621-letter "DNAString" instance seq: N ...
written 20 months ago by Matthias Lienhard140

Latest awards to Matthias Lienhard

Scholar 12 months ago, created an answer that has been accepted. For A: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

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