User: felipead66
felipead66 • 40
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Posts by felipead66
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... You are right regarding the RNA Seq, what I should clarify though is that I have single-cell RNA Seq therefore I could not limit to those common choices. Moreover, I have normalized data rather than gene counts. ...
written 3 days ago by
felipead66 • 40
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... I have RNA Seq for 2 groups of patients, Group1 with 4 patients and Group 2 with 5 patients. I want to find differences between the two groups (Grouo1 vs Group2) as well as whether a gene is up- or down regulated in one group vs the other. A first thought would be to use the Mann-Whitney test.
In ...
written 3 days ago by
felipead66 • 40
• updated
3 days ago by
ATpoint ♦ 26k
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... ##gff-version 3
Pav_co3988703.1 augustus gene 1 195 0.7 - . ID=Pav_co3988703.1_g010.1.br;Note=PREDICTED: disease resistance protein RPM1-like
Pav_co3988703.1 augustus exon 16 195 . - . ID=Pav_co3988703.1_g010.1.br:exon:1;
Parent=Pav_co3988703.1_g010.1.br
Pav_co3988703.1 augustus CDS 16 195 ...
written 21 days ago by
felipead66 • 40
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... My question may seem quite stupid but I run
pip install HTSeq
in my ubuntu machine and installation was successfully completed.
My problem is that now I cannot find HTSeq anywhere in order to use it.
Where does pip installation places HTSeq? ...
written 22 days ago by
felipead66 • 40
• updated
22 days ago by
Mensur Dlakic • 2.5k
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... No, I am referring to [this turorial][1]. My concern is how to make the GeneAnnotation.csv file for human data. Otherwise which human annotation file (a link) should I use.
[1]: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-04-Interfacing.pdf ...
written 4 weeks ago by
felipead66 • 40
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... Yes, I understand the metadata column. What I need is (1) a file to start with i.e. a human annotation file and (2) which column(s) of this file is necessary for creating the metadata.
My expression file includes gene name as an identifier. ...
written 4 weeks ago by
felipead66 • 40
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... Could you tell me the steps on how to do this? ...
written 4 weeks ago by
felipead66 • 40
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... I am trying to run WGCNA analysis for human expression data. Specifically I want to do the module annotation. How do I get an annotation .csv file (like the one in the [tutorials][1]) for human data?
[1]: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ ...
written 4 weeks ago by
felipead66 • 40
• updated
4 weeks ago by
Kevin Blighe ♦ 52k
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... I have a multi-sample vcf file annotated with snpeff.
I want to calculate the linkage disequilibrium.
I have 2 questions:
1. I use vcftools, in particular `./vcftools --vcf input_vcf.vcf --geno-r2 --out output` and it takes forever (it runs a week and keeps on). Is this OK?
2. Is it appropria ...
written 6 months ago by
felipead66 • 40
• updated
6 months ago by
RamRS ♦ 25k
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... Is it possible to extract the fasta sequences of specific genes from a snpeff output (vcf) file?
...
written 6 months ago by
felipead66 • 40
Latest awards to felipead66
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10 weeks ago,
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10 weeks ago,
asked a question with at least 3 up-votes.
For VariantFiltration warning "undefined variable"
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