User: Gungor Budak

gravatar for Gungor Budak
Gungor Budak240
Reputation:
240
Status:
Trusted
Location:
Ankara/Turkey
Website:
https://www.gungorbuda...
Twitter:
gungorbudak
Scholar ID:
Google Scholar Page
Last seen:
2 hours ago
Joined:
7 years, 11 months ago
Email:
g******@gmail.com

Bioinformatics Analyst at Seven Bridges & PhD Student at METU

Posts by Gungor Budak

<prev • 21 results • page 2 of 3 • next >
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Comment: C: Integrated genome browser, how to add exons?
... @omer.k Sure, just make sure you have the correct format. Filename or the extension won't matter but I suggest you keep the extension as `.bed`, instead of `.txt` which can be done using Notepad on Windows. However, you should also consider installing a better text editor such as [Atom][1]. [1]: ...
written 2.5 years ago by Gungor Budak240
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Answer: A: Where can I get fastq sequence files of length 150 and more.
... Use [Sequence Read Archive][1] advanced search and provide read length as 150 and species as Homo sapiens. You can add more filters if you want. The query should look something like this: ``` (150[ReadLength]) AND "Homo sapiens"[orgn:__txid9606] ``` And here is [a result for paired-end sequencing ...
written 2.5 years ago by Gungor Budak240
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Answer: A: Integrated genome browser, how to add exons?
... You just make [a BED][1] file for your gene in one line and specify exon locations. For example, Say your gene starts from chrY position 1000 and ends at chrY position 5000 and has two exons from position 1000 with size 250 and position 4500 with size 500. So the BED file should have the following ...
written 2.5 years ago by Gungor Budak240
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Answer: A: SDF data from pubchem database by entering SID or CID of molecule
... You can use [PubChemPy Python wrapper][1] for PUG REST API: import pubchempy as pcp pcp.download('SDF', '5090.sdf', 5090, 'cid') So above code downloads an SDF file for compound with [CID 5090][2]. [1]: http://pubchempy.readthedocs.io/en/latest/guide/introduction.html [2]: https://pub ...
written 3.3 years ago by Gungor Budak240
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Comment: C: Extract some features from a combined gene bank file in bash
... Check out this answer: https://www.biostars.org/p/96412/#96455 It uses `sed`. But I suggest you learn BioPython, it's much more expressive and easy. ...
written 3.6 years ago by Gungor Budak240
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Comment: C: Extract some features from a combined gene bank file in bash
... Thanks, this is helpful. I'm not sure but SeqIO might also read multi-genbank format. But she might also download them again (very small files although I don't know how many she has). ...
written 3.6 years ago by Gungor Budak240
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Answer: A: please someone help me to extract some features from a combined gene bank file i
... You can use BioPython for that. But don't merge GB files, keep them individual and read them one by one using BioPython and extract the information. Check out below example code for [NC_005816][1]: from Bio import SeqIO record = SeqIO.read('NC_005816.gb', 'genbank') for featur ...
written 3.6 years ago by Gungor Budak240
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Answer: A: Eland format to Bed format?
... I believe this is already a BED-formatted text file and the scores for the peaks are in the fifth column. These peaks are called using HPeak and in their documentation they state: `.allregions.txt`: This is the old main output file (in version 1.0 and 1.1). It is in BED format (no strand) indicatin ...
written 4.5 years ago by Gungor Budak240 • updated 5 months ago by RamRS27k
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Comment: C: Get Exons & Introns Using Ensembl Rest Api
... Yes, I have. And started watching tuts and doing exercises. It'll definitely help. Thanks ...
written 6.5 years ago by Gungor Budak240
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Comment: C: Get Exons & Introns Using Ensembl Rest Api
... REST API is really cool, I can't wait to see it fully functional. I'll try Perl API. Actually, I installed it but I got lost in Perl classes and data types. And it seemed a bit slow. But if it's the only option, I will look at it again and tell you if I have questions. Thanks Emily. ...
written 6.5 years ago by Gungor Budak240

Latest awards to Gungor Budak

Scholar 23 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Scholar 24 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Where can I get fastq sequence files of length 150 and more.
Scholar 24 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Where can I get fastq sequence files of length 150 and more.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Get Exons & Introns Using Ensembl Rest Api

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