User: brunobsouzaa
brunobsouzaa • 180
- Reputation:
- 180
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- Location:
- Brazil
- Last seen:
- 10 hours ago
- Joined:
- 5 years, 1 month ago
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Posts by brunobsouzaa
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... 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 ...
written 2 days ago by
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
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... I think [this post][1] will have your answer!
[1]: https://www.biostars.org/p/301684/ ...
written 6 weeks ago by
brunobsouzaa • 180
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... 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
brunobsouzaa • 180
Latest awards to brunobsouzaa
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For A: Bash script for calling CNVs using cnvkit
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created a question with more than 1,000 views.
For Trying to visualize .bed file
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For Doubt on filtering data from .VCF file
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