User: morovatunc

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morovatunc460
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Turkey
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mortunco
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11 hours ago
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Posts by morovatunc

<prev • 194 results • page 1 of 20 • next >
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Comment: C: Transcription Factor Specific Mutation Signature Enrichment
... hello we used cosine similarity for the comparsion in my second question. https://www.nature.com/articles/s41467-020-14644-y please see the method. Also there are more packages came up after that time so you should be checking deconstructSig too. good luck ...
written 4 months ago by morovatunc460
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Answer: C: Getting this information from WGS
... The cleanest way would be getting bam file and calculating average read depth. If you dont have an access to this, variant callers provide depth value. So my suggestion would be to parse that each call in the VCF to calculate average. But I would be careful while doing this because callers usually ...
written 4 months ago by morovatunc460
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Comment: C: How to calculate dinucleotide A/T patterns in a given human reference genome reg
... consensusMatrix(dinucleotideFrequency(DNA.set)) ? maybe ? ...
written 20 months ago by morovatunc460
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Comment: C: How to calculate dinucleotide A/T patterns in a given human reference genome reg
... dinucleotideFrequency function of biostrings could give those 2mers. than you can take the subset of your desired ones. ...
written 20 months ago by morovatunc460
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Comment: C: Finding Chip Seq Overlaps with Bed files
... "based on my experience" ...
written 20 months ago by morovatunc460
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Answer: A: Finding Chip Seq Overlaps with Bed files
... For the ones who has not found an answer. Homer's mergePeak function exactly what I want. Link itself is pretty explanatory. http://homer.ucsd.edu/homer/ngs/mergePeaks.html However, author seems not to respond problems related with the software so heads up. ...
written 20 months ago by morovatunc460
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Answer: A: IGV/IGB add two lines in a track
... Hi. For bigwigs, I think you can use IGV's Overlay Tracks function. So select your tracks, right click and choose Overlay Tracks from right click menu. These are the screen shots. https://ibb.co/nQsmWL https://ibb.co/kUB25f Hope this helps, Tunc. ...
written 23 months ago by morovatunc460
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Comment: C: FIMO output that preserves padj values
... I think your method is much better. ...
written 2.0 years ago by morovatunc460
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Comment: C: FIMO output that preserves padj values
... I dont have your data at the moment therefore I cannot give explicit solution but I can show you the way R has a function called merge.data.frame. We are gonna use this to merge your initial data with the latest fimo output. So In the end you will have BED + fimo merged together. (probably, you wil ...
written 2.0 years ago by morovatunc460
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Amplicon based sequencing Mutation Calling
... Dear all, We are investigating the effect of TF-mediated mutations on genome. In the validation part, we narrowed our regions to 1. We sequenced this region and upstream of it and obtained ~100 k coverage with paired end reads. This is our experimental setup. So we simple want to compare mutation f ...
sequence mutation calling sequencing written 2.1 years ago by morovatunc460

Latest awards to morovatunc

Popular Question 4 weeks ago, created a question with more than 1,000 views. For VarDictJava BED file input Problem
Popular Question 11 weeks ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 12 weeks ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 3 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 3 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Binding sites of annotated chip-seq peak files
Scholar 4 months ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files
Popular Question 6 months ago, created a question with more than 1,000 views. For VarDictJava BED file input Problem
Popular Question 6 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 7 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 7 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 8 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 10 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 16 months ago, created a question with more than 1,000 views. For Variant Calling output problem GL000 contigs
Popular Question 16 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 16 months ago, created a question with more than 1,000 views. For HOMER mergePeaks -d value definition
Popular Question 16 months ago, created a question with more than 1,000 views. For About Dream Challenge Somatic Mutation Calling Algorithms
Popular Question 16 months ago, created a question with more than 1,000 views. For Mutational Calling with SomaticSeq
Popular Question 16 months ago, created a question with more than 1,000 views. For VarDictJava BED file input Problem
Popular Question 17 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 17 months ago, created a question with more than 1,000 views. For VarDictJava BED file input Problem
Popular Question 17 months ago, created a question with more than 1,000 views. For Variant Calling output problem GL000 contigs
Popular Question 18 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 19 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information

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