Moderator: Charles Warden
Charles Warden ♦ 7.7k
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- Duarte, CA
- Website:
- https://sites.google.c...
- Twitter:
- @cwarden45
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- Last seen:
- 23 hours ago
- Joined:
- 6 years, 12 months ago
- Email:
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I am a Bioinformatics Specialist at City of Hope, where I work in the Integrative Genomics Core doing microarray and high-throughput sequencing analysis.
However, the feedback that I provide represent my own personal opinions.
Posts by Charles Warden
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... It would probably be best to look for similar results in more samples.
However, what I can say is that different methods had similar results for the HLA-A, HLA-B, and HLA-C genes for myself, but I got different results for the HLA-D genes.
If you consider the HLA types defined from the 2 SNPs, tha ...
written 6 days ago by
Charles Warden ♦ 7.7k
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Comment:
C: Converting TPM to FPKM
... I think the concern is that you may not be able to directly convert them.
For example, I may calculate FPKM from unique alignments from htseq-count and CPM from the sum of transcript counts for the same gene (with estimations that try to correctly assign multi-mapped genes). In that situation, I c ...
written 19 days ago by
Charles Warden ♦ 7.7k
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... I have some notes on courses that I have either taken or are considering taking in the future:
http://cdwscience.blogspot.com/2019/12/experiences-with-on-line-courses.html
I am not sure what level of analysis you are trying to obtain proficiency in. I have some notes on a couple JHU Coursera Data ...
written 28 days ago by
Charles Warden ♦ 7.7k
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... **Update (4/28/2010)**: When I was BLASTing an assembly, I noticed that the issue of non-PhiX top BLAST hits for PhiX sequence has come up again.
As of today, I could see that for this sequence:
>PhiX_test
CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
Unfortuna ...
written 29 days ago by
Charles Warden ♦ 7.7k
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... FYI, I have completed some testing with STITCH, which I think looks reasonable good (as an open-source option, given that Gencove will require a license after the free trial, and they check to get some sense of how many samples you will process during that free trial):
![enter image description her ...
written 7 weeks ago by
Charles Warden ♦ 7.7k
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... In general, there are some jobs where I would expect less change/research, such as a PhD in Clinical Psychology becoming a Psychologist (even though there are now a lot of social workers with a MSW or other qualification to be a Licensed Clinical Social Worker).
I think the minimum requirement for ...
written 3 months ago by
Charles Warden ♦ 7.7k
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... Thank you for the response.
However, I think Lior's tweet may have been misunderstood. He is calling such an application *pseudoscience* because of the likelihood that individuals can make claims that are not actually very robust and/or have limited predictive power. While it would be desirable t ...
written 3 months ago by
Charles Warden ♦ 7.7k
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... I apologize that I don't have more specific advice to provide.
In industry, my understanding is that experience can help. For example, I thought that I have seen jobs where you might be able to get a job with a PhD in Bioinformatics or an MS in Bioinformatics + 5-10 years of experience. For other ...
written 3 months ago by
Charles Warden ♦ 7.7k
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... I've dropped out of 2 PhD programs, and I am still debating a somewhat similar question.
I think finding the right way to represent your abilities is important. So, if you have concerns about the ability to build off what you are doing for long-term plans, then I think you should take that serious ...
written 3 months ago by
Charles Warden ♦ 7.7k
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... Thank you!
I sent them an e-mail (to **support@gencove.com**) relatively recently (I believe a little less than a month ago) with a slightly different question (even though it contained a portion asking about free use of GENCOVE), and I haven't heard back.
I am thinking about looking into the free ...
written 3 months ago by
Charles Warden ♦ 7.7k
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