User: brunobsouzaa

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brunobsouzaa180
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180
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Location:
Brazil
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10 hours ago
Joined:
5 years, 1 month ago
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b***********@gmail.com

Posts by brunobsouzaa

<prev • 46 results • page 1 of 5 • next >
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Question on Bonferroni correction
... Hi Everyone. So, my question is quite simple but raises me a little doubt. I have a data like the following: Patient Sex Age SNP1 SNP2 SNP3 SNP4 Outcome 1 M 56 TT CC AG AT 1 2 M 47 AT CG AA AA 0 3 F 85 AA GG AA AA 1 4 M 90 TT GG AG TT 0 5 M 75 TT GG ...
bonferroni p-values written 2 days ago by brunobsouzaa180
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Comment: C: Help with my differential expression analysis (homework)
... I agree with you... Hope OP realizes that my code will NOT work for what he is intended but, will force him to at least read the documentation and do a more deep search into the subject! ...
written 6 days ago by brunobsouzaa180
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Comment: C: Help with my differential expression analysis (homework)
... Try using STAR for your alignment! For the count tables, Rsubreads is perfect for the job, just take a look into the manual, it's pretty easy! I'll leave my code here, maybe it works for you... library(Rsubread) files <-c("path/to/file_1.bam", "path/to/file_2.bam", "path/to/file_3.bam", ...
written 7 days ago by brunobsouzaa180
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Comment: C: cnvkit Error message "length of weights should be the same as the number of prob
... Hey man... Do you have the solution for this issue? I'm asking because I'm having the exact same error! ...
written 7 days ago by brunobsouzaa180
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Comment: C: Interval list for GATK tool Haplotype Caller
... Yes, you can specify a interval list, just use the `-L` option and point to a BED file containing your intervals! ...
written 21 days ago by brunobsouzaa180
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Answer: A: Converting SNPs from hg19 to hg38
... You could map your variants using [VEP][1]. Just upload the SNPs list! [1]: https://www.ensembl.org/Tools/VEP ...
written 28 days ago by brunobsouzaa180
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Answer: A: local ancestry in admixed populations
... As far as I know, you could use STRUCTURE or EIGENSTRAT for such task. There's also [LAMP][1], which I think would give you exactly what you need! [1]: http://lamp.icsi.berkeley.edu/lamp/ ...
written 28 days ago by brunobsouzaa180
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Answer: A: How to generate a bed file from X:21915521-21918496 list
... There's so many options for this task. I would use `sed -e 's/:/\t/g' -e 's/-/\t/g'` ...
written 5 weeks ago by brunobsouzaa180
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Answer: A: How can get overlap size in bedtools multi-intersect?
... I think [this post][1] will have your answer! [1]: https://www.biostars.org/p/301684/ ...
written 6 weeks ago by brunobsouzaa180
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Comment: C: Error: Could not find or load main class -Xmx4g
... Yes, I have read the readme file... Also noticed that OP is starting into this kind of analysis. I'm not saying that his syntax is wrong, just gave him an alternative option to realize that he can run GATK without CD into the tool folder or include the file into his `$PATH` ...
written 9 weeks ago by brunobsouzaa180

Latest awards to brunobsouzaa

Scholar 11 months ago, created an answer that has been accepted. For A: Bash script for calling CNVs using cnvkit
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Trying to visualize .bed file
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Doubt on filtering data from .VCF file

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