User: morovatunc

gravatar for morovatunc
morovatunc400
Reputation:
400
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Trusted
Location:
Turkey
Twitter:
mortunco
Last seen:
2 weeks, 2 days ago
Joined:
4 years, 9 months ago
Email:
m*********@gmail.com

Posts by morovatunc

<prev • 192 results • page 1 of 20 • next >
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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 14 months ago by morovatunc400
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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 14 months ago by morovatunc400
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Comment: C: Finding Chip Seq Overlaps with Bed files
... "based on my experience" ...
written 15 months ago by morovatunc400
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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 15 months ago by morovatunc400
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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 17 months ago by morovatunc400
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Comment: C: FIMO output that preserves padj values
... I think your method is much better. ...
written 19 months ago by morovatunc400
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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 19 months ago by morovatunc400
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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 19 months ago by morovatunc400
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Comment: C: Does anybody success to download data using icgc-storage-client ?
... I think you should write to ICGC help desk. They are very helpful. Also I suggest you to log in to the spesific ec2 region. As far as I know, USA ec2 servers have access to icgc data. Final thing, make sure you set your key code. (The code that lets you access to the restricted data.) ...
written 23 months ago by morovatunc400
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Comment: C: Starrseq data how can I characterise reads that maps out of the targeted regions
... Yeah. I think it is cap-starrseq because I remember the preparation of the array design, forward and reverse primers etc. (Sorry for my ignorance, I mainly focus on the computational part of this project.) Could you help me to understand why you are not very concerned with %70 unspecific mappings?( ...
written 23 months ago by morovatunc400

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 8 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
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Popular Question 11 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 11 months ago, created a question with more than 1,000 views. For Variant Calling output problem GL000 contigs
Popular Question 11 months ago, created a question with more than 1,000 views. For VarDictJava BED file input Problem
Popular Question 12 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 13 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
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Popular Question 15 months ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 15 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 15 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 17 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
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Popular Question 19 months ago, created a question with more than 1,000 views. For CRISPR screen Trimming with mageck low mappability

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