User: morovatunc

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morovatunc380
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380
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Location:
Turkey
Twitter:
mortunco
Last seen:
10 hours ago
Joined:
3 years, 3 months ago
Email:
m*********@gmail.com

Posts by morovatunc

<prev • 189 results • page 1 of 19 • next >
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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 2 days ago by morovatunc380
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Comment: C: FIMO output that preserves padj values
... I think your method is much better. ...
written 5 weeks ago by morovatunc380
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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 5 weeks ago by morovatunc380
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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 7 weeks ago by morovatunc380
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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 5 months ago by morovatunc380
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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 5 months ago by morovatunc380
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Comment: C: Starrseq data how can I characterise reads that maps out of the targeted regions
... qualimap is highly appreciated. I have been using it for 3 weeks in multiple projects. ...
written 5 months ago by morovatunc380
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Starrseq data how can I characterise reads that maps out of the targeted regions.
... Hi, We conducted starrseq experiment that measures the actives of the given library. (Say enhancers). Then, we send this data to WGS. **Background:** Mapping: We have ~250million reads with 150 bp paired end data. We used bowtie with -v 3 -m 1 —best —strata -X 2000 parameters. Then we analysed ...
starrseq alignment mapping sequencing written 6 months ago by morovatunc380
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Comment: C: Simplest output format of blast contamination check
... Yeah yeah you are totally right about the precaution beforehand. Currently, I am just doing this to check to find the most obvious ones. I dont want to mess with the default word size and mismatch levels. Is there way that I can make this tuning simpler? ...
written 8 months ago by morovatunc380
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Comment: C: Simplest output format of blast contamination check
... For the runs please see the reply on top. I have taken a look to blobtools paper. It seems to mine output of blast to make the graphs actually. blastn -outfmt "6 qseqid staxids bitscore std" -query kefal.contigs.fasta -db /mnt/compgen/inhouse/share/blastdb/nt -o kefal_canu_megablast.out ( th ...
written 8 months ago by morovatunc380

Latest awards to morovatunc

Popular Question 5 weeks ago, created a question with more than 1,000 views. For CRISPR screen Trimming with mageck low mappability
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Great Question 4 months ago, created a question with more than 5,000 views. For Kallisto New RNA-seq quantification method discussion
Popular Question 4 months ago, created a question with more than 1,000 views. For Homer mergePeaks : Cannot calculate the mean of overlapped peaks
Popular Question 4 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 5 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 6 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 6 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 11 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
Popular Question 11 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
Popular Question 11 months ago, created a question with more than 1,000 views. For IGV peak Visualation Problem
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 16 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 19 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 Kallisto New RNA-seq quantification method discussion
Popular Question 19 months ago, created a question with more than 1,000 views. For Visualization of Homer mergePeaks output Venn?
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