User: Gungor Budak
Gungor Budak • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- Ankara/Turkey
- Website:
- https://www.gungorbuda...
- Twitter:
- gungorbudak
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 days, 11 hours ago
- Joined:
- 8 years ago
- Email:
- g******@gmail.com
Bioinformatics Analyst at Seven Bridges & PhD Student at METU
Posts by Gungor Budak
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2
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... 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 2.0 years ago by
Gungor Budak • 240
1
vote
1
answer
1.6k
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1
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... 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 2.1 years ago by
Gungor Budak • 240
0
votes
0
answers
873
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0
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... 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 2.1 years ago by
Gungor Budak • 240
2
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0
answers
223
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0
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... Can you show the full code? `dic` seems to be an `int` not a `dict` so it doesn't have `keys`. ...
written 2.1 years ago by
Gungor Budak • 240
2
votes
1
answer
1.5k
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1
answers
... 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 2.1 years ago by
Gungor Budak • 240
2
votes
2
answers
860
views
2
answers
... 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 2.1 years ago by
Gungor Budak • 240
0
votes
0
answers
1.5k
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0
answers
... @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 2.1 years ago by
Gungor Budak • 240
4
votes
1
answer
1.3k
views
1
answers
... 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 2.1 years ago by
Gungor Budak • 240
1
vote
1
answer
792
views
1
answers
... 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 2.1 years ago by
Gungor Budak • 240
0
votes
1
answer
850
views
1
answers
... @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 2.6 years ago by
Gungor Budak • 240
Latest awards to Gungor Budak
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Where can I get fastq sequence files of length 150 and more.
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Where can I get fastq sequence files of length 150 and more.
Teacher
2.1 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
2.1 years ago,
created an answer that has been accepted.
For A: Where can I get fastq sequence files of length 150 and more.
Teacher
2.2 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
2.6 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
6.3 years ago,
created a question with more than 1,000 views.
For Get Exons & Introns Using Ensembl Rest Api
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