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User: Gungor Budak

gravatar for Gungor Budak
Gungor Budak • 230
Reputation:
230
Status:
Trusted
Location:
Ankara/Turkey
Website:
https://www.gungorbuda...
Twitter:
gungorbudak
Scholar ID:
Google Scholar Page
Last seen:
2 days, 19 hours ago
Joined:
6 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 1 of 3 • next >
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Answer: A: Remove duplicates in a Excel table summing values of associated cells
... Don't use Excel for this task, use Python to read the input line by line, keep every line in a dictionary (key: header, value: list of marker and cm) and every time you read a line with header that is already in the dictionary, update the values accordingly and just output the content of the diction ...
written 11 months ago by Gungor Budak • 230
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Answer: A: Visualizing exome Sequencing data for depth
... Hi! You can do this with `samtools depth` easily. `samtools depth` can work with multiple inputs and it generates such a file with the below command: Command (please see official docs for arguments, you will probably need to provide forward and reverse reads from BAMs separately) samtools de ...
written 11 months ago by Gungor Budak • 230
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Comment: C: Error message on cufflinks: ImportError
... Were you using a different Python version or virtual environment for the first batch? And did you change anything regarding the Python packages in between. It seems it cannot import a package. ...
written 12 months ago by Gungor Budak • 230
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Comment: C: check if my gene name exists in Kegg pathway
... Can you show the full code? `dic` seems to be an `int` not a `dict` so it doesn't have `keys`. ...
written 12 months ago by Gungor Budak • 230
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Answer: A: BioPython BLAST Records HSP Sequences
... Hi, - `hsp.query` shows the sequence that you are searching for in the BLAST database - `hsp.match` shows the matches between the query and the subject - `hsp.subject` is the matched part of the sequence in the BLAST database. For example, I obtained following portion of the [HSP90 protein][1] an ...
written 12 months ago by Gungor Budak • 230
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Answer: A: Protein domain sequence extraction with Python
... File 1 has some formatting issues. It should have a header and one or multiple sequence lines. Like this: >sp|P17672.2|E75BA_DROMERecName:Full=Ecdysone-inducedprotein75B,isoformA;Short=E75-B;AltName:Full=Nuclearreceptorsubfamily1groupDmember3,isoformA MVCAMQEVAAVQHQQQQQQLQLPQQQQQQQQTTQQQ ...
written 12 months ago by Gungor Budak • 230
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Comment: C: How to execute R Script from php exec() function
... @WouterDeCoster I believe this can still be a valid question for bioinformatics field. We sometimes need to do real-time analyses and build a web server for that. This web server can be built in PHP and run R scripts at backend and collect results and show it to the user. @anshulmbi As an answer, h ...
written 12 months ago by Gungor Budak • 230
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Answer: A: how to use bgzip with tabix docker image
... Considering you are at your project's folder with the input files that you want to pass to `bgzip`, use the following command to interactively run `bgzip` in a Docker container interactively and mounting the current directory under `/opt/` within the Docker container generate: docker run -ti -v ...
written 12 months ago by Gungor Budak • 230
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Answer: A: Fetching Genbank records and parsing them to be DNAStringset objects
... It seems `readDNAStringSet ` requires a path to the FASTA file rather than directly working with the object returned by `efetch`. A workaround I can think of is to write the content of the object to a file then read it using `readDNAStringSet` as follows; RABV.fa <- efetch("EU293116", db="nu ...
written 12 months ago by Gungor Budak • 230
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Comment: C: Integrated genome browser, how to add exons?
... @omar.k, for the question related to the line: No, it won't work this way. You can write the gene name to the fourth column and keep the gene's chromosome name in the first column. Otherwise, IGV won't know which chromosome to put your gene/exons on. ...
written 18 months ago by Gungor Budak • 230

Latest awards to Gungor Budak

Scholar 12 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Scholar 12 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Teacher 12 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 12 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Teacher 13 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 18 months ago, created an answer that has been accepted. For A: Where can I get fastq sequence files of length 150 and more.
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Get Exons & Introns Using Ensembl Rest Api
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