User: brunobsouzaa
brunobsouzaa • 260
- Reputation:
- 260
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- Brazil
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- an hour ago
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- 5 years, 3 months ago
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Posts by brunobsouzaa
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... For this kind of analysis, there's a few steps that you have to do (just checking what you've done so far!). Firts perform test for HWE then perform IBD. For your affection, plink will assume that this info is in a specific column of your ped file (check the manual). Just code it as 0 and 1 and you' ...
written 1 day ago by
brunobsouzaa • 260
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... Thank you very much, man! Upvoted! ...
written 8 days ago by
brunobsouzaa • 260
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60
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Comment:
C: error in using circos plot
... What command line have you used? ...
written 8 days ago by
brunobsouzaa • 260
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... Hi everyone. I'm studying two SNPs in a case/control study and one part of the analysis is to test for additive model. So the question is: Can I use logistic regression for this task or should I just build a 2x2 table and perform Fisher exact test?
The data looks like this:
Outcome SNP_1 SNP_2 ...
written 8 days ago by
brunobsouzaa • 260
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... Why don't you use Ensembl VEP to annotate your VCFs? ...
written 14 days ago by
brunobsouzaa • 260
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... I don't think this will work but you can try using `cnvkit` with a flat reference. Usually, you need more samples to build your baseline but doesn't hurt to try!!! ...
written 14 days ago by
brunobsouzaa • 260
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... Changing your align method is not going to solve your problem! Try running FastQC on all your R1 and R2 files before alignment and check data quality. ...
written 16 days ago by
brunobsouzaa • 260
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... How you annotate your VCFs? Ensembl VEP will output this for you, just use the `--stats_file` on the command line during annotation.
...
written 22 days ago by
brunobsouzaa • 260
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... So, if you did everything right, you need to investigate more deeply... That happened to me once and I discovered that, unfortunately, the problem was on the library prep. If you did this work will be easier for you to find the issue but, if not, investigate all metrics.
Second, make sure that you h ...
written 22 days ago by
brunobsouzaa • 260
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127
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Comment:
C: Merging BAM vs concatenate FASTQ
... Good question! I don't see this as a rule of what you have to do... I like to concatenate all my R1 and R2 files before alignment. But it should be fine to align your BAM files also! ...
written 28 days ago by
brunobsouzaa • 260
Latest awards to brunobsouzaa
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: How to analyze Illumina RNASeq data
Scholar
14 months ago,
created an answer that has been accepted.
For A: Bash script for calling CNVs using cnvkit
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For Trying to visualize .bed file
Popular Question
4.1 years ago,
created a question with more than 1,000 views.
For Doubt on filtering data from .VCF file
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