User: smilefreak

gravatar for smilefreak
smilefreak400
Reputation:
400
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Trusted
Location:
New Zealand
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Google Scholar Page
Last seen:
2 years ago
Joined:
4 years, 6 months ago
Email:
s******@gmail.com

MSc student at the University of Otago.
 

My research project has a focus on the origin and function of copy-number variation in eukaryotic genomes. 

 

Posts by smilefreak

<prev • 41 results • page 1 of 5 • next >
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Comment: C: GGplot adding scales under specific graphs.
... I was searching using the incorrect keywords. Thanks! ...
written 2.8 years ago by smilefreak400
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GGplot adding scales under specific graphs.
... I am trying to create a visualisation of read-length distribution using ggplot2, but I have an awkward prime-number of samples ( 17 ), so I cannot get scales underneath each column.  Does anyone know how I would add x scales to the MS10134, MS10135, and MS10136 samples specifically. If I change th ...
R ngs ggplot2 written 2.8 years ago by smilefreak400 • updated 2.8 years ago by David W4.6k
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Resequencing region selection
... Hi All, I have been given some data from a candidate gene resequencing experiment. I have recently noticed that processed transcipts are included in the regions. As far as i understand a processed transcript is not thought to code for protein. Does any one think this could have any downstream affec ...
exome ngs written 2.8 years ago by smilefreak400 • updated 2.8 years ago by Sean Davis24k
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Comment: C: What are the biggest challenges bioinformaticians have with data analysis?
... I would add maintain to user experience. I agree these are huge problems, but I think it a more symptomatic of publishing in biological journals and how the biological sciences measures researchers. The current system places pressure on researchers time and many are not willing to endure the extra w ...
written 3.2 years ago by smilefreak400
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Comment: C: Are we seeing a bioinformatician shortage?
... And don't forget the interesting problems! ...
written 3.2 years ago by smilefreak400
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Comment: C: What is reciprocal partners?
... Yep as my goto simplest explanation, the other possibility is that it is a fusion, which was validated in another tumour already so they decided not to do it again and just called it a true positive. However, to me a reciprocal partner gene means they traded DNA, just like the philadelphia chromosom ...
written 3.2 years ago by smilefreak400
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Comment: C: What is reciprocal partners?
... Reciprocal partners are the genes that are fused with your target gene as far as I can tell, so that would the gene that fused with ALK and/or ROS1.  My interpretation is that if they used experimental methods, but if it represented the other fusion then they would use that without validation. 5' ...
written 3.2 years ago by smilefreak400
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Comment: C: RNAseq Read length distribution FFPE
... FFPE samples will contain degraded RNA, so it is not unlikely that the may contain many short sequences. The patterns should be somewhat similar to ancient DNA patterns, so maybe assessing these using the mapDamage tool could be useful. https://github.com/ginolhac/mapDamage (mapDamage) http://www. ...
written 3.2 years ago by smilefreak400
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Comment: C: Problem is to design model matrix for edgeR
... As Devon say below label serves no purpose, when trying to generate the design.matrix you need more than one level, other wise R cannot create the model representation.  ...
written 3.2 years ago by smilefreak400
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Answer: A: subset fastq file
... python solution using list comprehensions.  160 = 40 * 4 and 156,157, 158,159 are the indexes of the 40th line in the fastq file. #!/usr/bin/env python with open('reads.fastq') as f: with open('output.fastq) as out: [out.write(line) if (i % 160 in [156,157,158,159]) for i, line in enu ...
written 3.2 years ago by smilefreak400

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Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What are the biggest challenges bioinformaticians have with data analysis?
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: What are the biggest challenges bioinformaticians have with data analysis?
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Are we seeing a bioinformatician shortage?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What are the biggest challenges bioinformaticians have with data analysis?
Scholar 3.2 years ago, created an answer that has been accepted. For A: fasta file not compatible with SIFT?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What are the biggest challenges bioinformaticians have with data analysis?
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Student 3.2 years ago, asked a question with at least 3 up-votes. For BWA MEM and ancient DNA
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