User: YaGalbi

gravatar for YaGalbi
YaGalbi1.1k
Reputation:
1,120
Status:
Trusted
Location:
Biocomputing, MRC Harwell Institute, Oxford, UK
Website:
https://github.com/roo...
Last seen:
4 hours ago
Joined:
1 year, 10 months ago
Email:
r**********@gmail.com

Microbiology BSc Hons 2016

Bioinformatics MSc Distinction 2017

Bioinformatics Prize 2017

Posts by YaGalbi

<prev • 334 results • page 1 of 34 • next >
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Comment: C: Extracting upstream and Downstream of a Gene based on different intervals
... To do something like this in the past, I began by retrieving the TSS locations for all genes from Ensembl Biomart. I then wrote a simple AWK command like the one in the link provided by @genomax to get exactly what I want, using the TSS positions as the starting location. EDIT: With sachas answer ...
written 12 hours ago by YaGalbi1.1k
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Comment: C: Why does inclusion of decoy sequences cause more BWA alignments to an autosome?
... I don;t know why the decoy is doing this but I just wonder is there something about chromosome 6? I'd like to ask have you loaded the region in IGV? Are they all mapping to a very small region? Recently, I also found a very strange behaviour of reads from both ATAC-seq and ChiP-seq data mapping to ...
written 2 days ago by YaGalbi1.1k
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Comment: C: Find out point mutations or SNPs
... BLAST is not suitable for this. This is not what #finswimmer meant by "alignment". BLAST simply takes a short query sequence and aligns it to a database to look for similar sequences to identify the origin of the query sequence. But you are looking at an entire genome. What you need is an "aligner" ...
written 4 days ago by YaGalbi1.1k
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Answer: A: How to edit count matrix of a DESeq object?
... Apart from the [documentation][1], I suggest posting this in [Bioconductor][2]. [1]: https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/counts [2]: https://support.bioconductor.org ...
written 4 days ago by YaGalbi1.1k
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Comment: C: Swiss-Model vs. Modeller
... They are both excellent modelling programs. I wouldn't worry about any difference in quality. At the end of the day every model will require refinement after using evaluation tools. No modelling software will get it right first time. Swiss model, because of the online user interface, is far more u ...
written 8 days ago by YaGalbi1.1k
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Answer: A: A dataset containing small RNA-seq experiments over different tissues of human.
... Yes of course. There are loads. One easy example is the sequence read archive (SRA). 1) Go to [SRA][1] 2) Search term: "Homo sapiens"[orgn:__txid9606] 3) Filters: Public, RNA, and either exome or genome 4) Click the link to "Send results to Run Selector" 5) Play around with the facets (filter) ...
written 8 days ago by YaGalbi1.1k
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Comment: C: Same code for different versions of the same platform
... Try it and find out. ...
written 17 days ago by YaGalbi1.1k
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Comment: C: download from SRA
... Did you read the tutorial? [How to download raw sequence data from GEO/SRA][1] [1]: https://www.biostars.org/p/111040/ ...
written 17 days ago by YaGalbi1.1k
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Comment: C: Idea about increasing coverage in sequencing
... Why do you need so much coverage? ...
written 17 days ago by YaGalbi1.1k
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Comment: C: There any tools for gene regulation network visualizing?
... How dose [TRRUST][1] compare to [STRING][2]? Cytoscape is definetly the way to go: [OmicsAnalysisCollection][3] [Other network analysis apps][4] [1]: http://www.grnpedia.org/trrust/ [2]: https://string-db.org/ [3]: http://apps.cytoscape.org/apps/omicsanalysiscollection [4]: http://apps. ...
written 10 weeks ago by YaGalbi1.1k

Latest awards to YaGalbi

Voter 3 days ago, voted more than 100 times.
Popular Question 11 days ago, created a question with more than 1,000 views. For Rshiny - How do I check if user input exists in my data set?
Popular Question 15 days ago, created a question with more than 1,000 views. For Rshiny - How do I check if user input exists in my data set?
Popular Question 23 days ago, created a question with more than 1,000 views. For Quantile normalisation: raw rpkm or log2rpkm?
Popular Question 24 days ago, created a question with more than 1,000 views. For Rshiny - How do I check if user input exists in my data set?
Autobiographer 11 weeks ago, has more than 80 characters in the information field of the user's profile.
Popular Question 3 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Commentator 4 months ago, created a comment with at least 3 up-votes. For A: wig files to bigwig using UCSC kent
Guru 4 months ago, received more than 100 upvotes.
Scholar 6 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Scholar 6 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Popular Question 6 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Scholar 6 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Popular Question 11 months ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
Scholar 11 months ago, created an answer that has been accepted. For C: Displaying genes in genome browsers
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Looking for an annotation tool
Student 12 months ago, asked a question with at least 3 up-votes. For Is annotation of enhancers to nearest gene pointless?
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Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Looking for an annotation tool

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