User: Irsan

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Irsan7.1k
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PhD-student at Clinical Genetics, VU medical centre

Posts by Irsan

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Comment: C: How to get counts of STAR output (sam/bam).
... Hmm I still use star + htseq. I need to update my star version ...
written 4.0 years ago by Irsan7.1k
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Answer: A: How to get counts of STAR output (sam/bam).
... [HTseq][1] is another popular option [1]: http://www-huber.embl.de/HTSeq/doc/overview.html ...
written 4.0 years ago by Irsan7.1k
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Why does GISTIC require a markers file?
... In order to run [GISTIC(2.0)][1], you need at least: 1. Segmented copy numbers (.seg file, e.g. CBS output) 2. Gene annotation file in GISTIC format (refgene file) 3. A markers file that gives the genomic position of probes/windows that was used (before segmentation) I wonder what GISTIC does w ...
gistic copy number written 4.0 years ago by Irsan7.1k • updated 3.9 years ago by neelablore0
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Comment: C: csv into genome browser
... Then make sure you have a VCF file, because that is the standard format for SNVs. IGV can import and visualize VCFs. ...
written 4.0 years ago by Irsan7.1k
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Comment: C: csv into genome browser
... A csv file can contain anything. What kind of data are you talking about? single nucleotide variants/insertions & deletions, copy number, chipseq, methylation? ...
written 4.0 years ago by Irsan7.1k
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Answer: A: CNV detection analysis using R or Matlab
... Use the off-target data to do copy number analysis, for example with CopyWriteR. Alo see this post: https://www.biostars.org/p/139385/ ...
written 4.0 years ago by Irsan7.1k
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Blog: General recommendations for cancer genomics studies
... Dear fellow cancer researchers, In the last few years I have been working as a bio-informatician in a PhD-project aimed at improving retinoblastoma treatment and diagnosis through genomic characterization of human and murine tumor samples. Although retinoblastoma was my main project, I have been i ...
recommendations blog genomics cancer written 4.0 years ago by Irsan7.1k • updated 2.5 years ago by KevinL20
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Comment: C: Co-variants in differential expression analysis
... Do you know what you mean with co-variants? If you do, you should really be able to figure it out by reading the edgeR and/or limma vignettes like Devon said. ...
written 4.0 years ago by Irsan7.1k
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Comment: C: mutation signature in cancer
... What people mean with a mutation signature varies a lot. I see that after you have explained that you mean the signatures defined by cosmic you got a useful answer. But still it is unclear for example whether you managed to process reads to variants, which is required input for the suggested prog ...
written 4.1 years ago by Irsan7.1k
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Comment: C: Can I identify differential expressing genes of 2 samples using only 4 chips?
... yes, that is possible. It is also very well possible that the power of your analysis is low. It also seems like you have 2 technical replicates per condition, which is a waste of money. If you have only one biological replicate, it is still possible to see what genes are differentially expressed bet ...
written 4.1 years ago by Irsan7.1k

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Great Question 10 weeks ago, created a question with more than 5,000 views. For Disable Soft-Clipping Bwa Aln
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Titv Meaning
Scholar 10 weeks ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Scholar 10 months ago, created an answer that has been accepted. For A: Best Way To Quantify Influence Of Different Covariates On Gene Expression?
Scholar 10 months ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Scholar 10 months ago, created an answer that has been accepted. For A: Method to detect gene co-expression of genomic feature in cell lineage
Scholar 10 months ago, created an answer that has been accepted. For A: Why Cannot Limma Package Do Differential Expression Between Two Samples Without
Popular Question 10 months ago, created a question with more than 1,000 views. For Cancer genomics journals
Scholar 10 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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Scholar 2.4 years ago, created an answer that has been accepted. For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Cancer genomics journals
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Fastq Format Redundancy
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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Fastq Format Redundancy
Good Answer 2.7 years ago, created an answer that was upvoted at least 5 times. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
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