User: Irsan

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Irsan7.2k
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Amsterdam
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PhD-student at Clinical Genetics, VU medical centre

Posts by Irsan

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Comment: C: How do you get input files to a cromwell server
... Hi Geraldine (I think??), How do I make the cromwell server machine recognize the client/submission machine's file system? For example, do you recommend to to make my data directory on the client shareable over the network (SMB/CIFS), or can I adapt the URI string in my input file to something that ...
written 3 months ago by Irsan7.2k
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How do you get input files to a cromwell server
... I make use of cromwell in server mode to execute bioinformatics data processing pipelines written in widdle (.wdl = workflow description language). The machine from which I submit workflows is not the same as the machine that hosts the cromwell server (so a remote cromwell server). The input files f ...
workflow cromwell widdle wdl written 3 months ago by Irsan7.2k • updated 3 months ago by vdauwera960
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Comment: C: Workshop: Data manipulation and visualization with Python (3 places left)
... From now, 2 places left! Just signed up for the course. Looks promising! ...
written 3.5 years ago by Irsan7.2k
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Comment: C: Fastq Convert To Fasta
... OK, I have changed fasta to fastq ...
written 3.8 years ago by Irsan7.2k
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Answer: A: Heatmap trouble in R
... Because it scales the data. Use the scale="none" option ...
written 3.8 years ago by Irsan7.2k
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Comment: C: Is microarray gene expression analysis is dead ?
... Oh yeah that's right, forgot about that... ...
written 3.9 years ago by Irsan7.2k
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Comment: C: How to draw lego plot Using Mutation Data (MAF format input)?
... I would advice against it. Becuase of the three dimensions, some bars can block others. ...
written 3.9 years ago by Irsan7.2k
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Answer: A: Is microarray gene expression analysis is dead ?
... In research, micro-arrays are on their return but in clinical diagnostics they are still used a lot, in particular array-CGH or SNP-arrays to determine germ line CNVs that predispose to disease. ...
written 3.9 years ago by Irsan7.2k
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Comment: C: Calculate LogR ratio and BAF from X and Y intensities
... A sample for which you now the ploidy = 2. So any non-cancer sample would be fine. I think most of the time in a SNP-array run such a sample is included, for example a male and female reference DNA sample. It depends all on your research context but most of the time, best scenario is when you have a ...
written 4.1 years ago by Irsan7.2k
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Answer: A: Calculate LogR ratio and BAF from X and Y intensities
... BAF = Y / (X + Y) LRR = log2( (X + Y)sampleOfInterest / (X+Y)baselineSample) But you might want to do some normalization first, possbily with beadstudio or with tQn normalization. See here http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-409 ...
written 4.1 years ago by Irsan7.2k

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Scholar 12 weeks ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Titv Meaning
Great Question 5 months ago, created a question with more than 5,000 views. For Disable Soft-Clipping Bwa Aln
Scholar 5 months ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Scholar 12 months ago, created an answer that has been accepted. For A: Why Cannot Limma Package Do Differential Expression Between Two Samples Without
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Scholar 12 months ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Popular Question 12 months ago, created a question with more than 1,000 views. For Cancer genomics journals
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Scholar 12 months ago, created an answer that has been accepted. For A: any tool or R package for integrated analysis of miRNA and mRNA expression data
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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Cancer genomics journals
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