User: burcakotlu

gravatar for burcakotlu
burcakotlu40
Reputation:
40
Status:
New User
Location:
Turkey
Last seen:
10 months, 3 weeks ago
Joined:
6 years, 4 months ago
Email:
b*********@gmail.com

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Posts by burcakotlu

<prev • 47 results • page 1 of 5 • next >
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Why download GRch38 when my selected filter is only hg19 from ENCODE Data Experiment Matrix?
... I'm downloading histone ChIp-Sep from ENCODE Data Experiment Matrix. I'm selecting genome assembly as hg19. Why it is downloading also GRch38 data? Any idea? ...
data encode experiment matrix written 10 months ago by burcakotlu40
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Comment: C: Is there a file information dictionary for files downloaded from ENCODE through
... Thanks. That metadata.csv is also downloaded. But I was not aware of. Thanks, again. ...
written 10 months ago by burcakotlu40
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Is there a file information dictionary for files downloaded from ENCODE through batch download?
... e.g: I have downloaded ENCFF212JTP.bigwig and many others using batch download. Can we learn that ENCFF212JTP.bigwig comes from H3K27ac histone marks from MCF-7 cell line using a dictionary in code? Instead of visiting web page for each file https://www.encodeproject.org/files/ENCFF212JTP/ man ...
encode batch downoad written 10 months ago by burcakotlu40 • updated 10 months ago by prince2612199170
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Comment: C: What is the difference between tissues and cell lines in ENCODE>
... Yes, I think so. When I search for some cell lines in https://www.atcc.org/ they came out to be all cancer cell lines. But tissues seem to be from normal donors. But, of course I could not do this verification for all. Thanks. ...
written 10 months ago by burcakotlu40
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Comment: C: What is the difference between tissues and cell lines in ENCODE>
... What I have is cancer tissues across many tissues. But I do not know whether tissues in ENCODE come from normal tissues or cancer tissues. ...
written 10 months ago by burcakotlu40
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What is the difference between tissues and cell lines in ENCODE>
... I want to download histone modifications and transcription factor binding sites data from ENCODE. In this link below: https://www.encodeproject.org/matrix/?type=Experiment&status=released There are tissues and cell lines, from which of them I should download data? Thanks, Burcak ...
cell line encode written 10 months ago by burcakotlu40
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Comment: C: Can there be overlaps in a bigWig or bigBed file?
... Thank you very much. ...
written 11 months ago by burcakotlu40
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Comment: C: Can there be overlaps in a bigWig or bigBed file?
... Thanks for the paper for reference. For BigBed files, it writes that it can contain overlapping intervals. Is there such an information for BigWig files? I could not see in that paper. Thanks again. ...
written 11 months ago by burcakotlu40
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Can there be overlaps in a bigWig or bigBed file?
... Hi to all, Can there be overlaps in a bigWig or bigBed file? Thanks in advance, Burcak ...
bigbed bigwig written 11 months ago by burcakotlu40 • updated 11 months ago by Alex Reynolds30k
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Answer: A: How to download *.FPKM-UQ.txt.gz files from TCGA GDC for some certain samples u
... Well I found out that using GDC Data Transfer tool is the best way to download data from GDC. https://gdc.cancer.gov/access-data/gdc-data-transfer-tool https://docs.gdc.cancer.gov/Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload/ These links were quite informative. Thanks, Burcak Otlu ...
written 2.9 years ago by burcakotlu40

Latest awards to burcakotlu

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Is there a file for AssemblyName 2 RefSeq Assembly Accession (ID) for homo sapiens?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Having problem with NCBI remap.pl
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Having problem with NCBI remap.pl
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Finding Rsids Of Snps For A Given Chrname, Start And End Positions For Grch37/Hg19
Popular Question 5.6 years ago, created a question with more than 1,000 views. For How To Get A Dbsnp Data From Java?
Scholar 5.7 years ago, created an answer that has been accepted. For A: Having problem with NCBI remap.pl

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