User: smilefreak
smilefreak • 400
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- 2 years, 9 months ago
- Joined:
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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
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... I was searching using the incorrect keywords. Thanks!
...
written 3.5 years ago by
smilefreak • 400
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... 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 ...
written 3.5 years ago by
smilefreak • 400
• updated
3.5 years ago by
David W ♦ 4.7k
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... 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 ...
written 3.5 years ago by
smilefreak • 400
• updated
3.5 years ago by
Sean Davis ♦ 25k
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... 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 4.0 years ago by
smilefreak • 400
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... And don't forget the interesting problems!
...
written 4.0 years ago by
smilefreak • 400
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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 4.0 years ago by
smilefreak • 400
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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 4.0 years ago by
smilefreak • 400
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... 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 4.0 years ago by
smilefreak • 400
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... 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 4.0 years ago by
smilefreak • 400
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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 4.0 years ago by
smilefreak • 400
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