User: morovatunc

gravatar for morovatunc
morovatunc390
Reputation:
390
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Trusted
Location:
Turkey
Twitter:
mortunco
Last seen:
17 hours ago
Joined:
3 years, 6 months ago
Email:
m*********@gmail.com

Posts by morovatunc

<prev • 193 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 1 day ago by morovatunc390
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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 1 day ago by morovatunc390
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Comment: C: Finding Chip Seq Overlaps with Bed files
... "based on my experience" ...
written 6 days ago by morovatunc390
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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 6 days ago by morovatunc390
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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 3 months ago by morovatunc390
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Comment: C: FIMO output that preserves padj values
... I think your method is much better. ...
written 4 months ago by morovatunc390
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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 4 months ago by morovatunc390
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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 4 months ago by morovatunc390
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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 8 months ago by morovatunc390
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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 8 months ago by morovatunc390

Latest awards to morovatunc

Popular Question 6 days ago, created a question with more than 1,000 views. For VCF filtration problem No genotype information
Popular Question 7 days ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 23 days ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 3 months ago, created a question with more than 1,000 views. For CRISPR screen Trimming with mageck low mappability
Popular Question 4 months ago, created a question with more than 1,000 views. For CRISPR screen Trimming with mageck low mappability
Popular Question 4 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Great Question 7 months ago, created a question with more than 5,000 views. For Kallisto New RNA-seq quantification method discussion
Popular Question 7 months ago, created a question with more than 1,000 views. For Homer mergePeaks : Cannot calculate the mean of overlapped peaks
Popular Question 7 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 8 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 9 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 10 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 12 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 14 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 14 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 14 months ago, created a question with more than 1,000 views. For IGV peak Visualation Problem
Popular Question 15 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 17 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 19 months ago, created a question with more than 1,000 views. For Chip-Seq Peak hight difference between BED and BW file formats.
Popular Question 22 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 22 months ago, created a question with more than 1,000 views. For Kallisto New RNA-seq quantification method discussion
Popular Question 22 months ago, created a question with more than 1,000 views. For Visualization of Homer mergePeaks output Venn?

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