User: felipead66

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felipead6640
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Posts by felipead66

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Which statistical test to use for two groups of patients?
... 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 felipead6640
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Which statistical test to use for two groups of patients?
... 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 ...
two_groups rna-seq statistics written 3 days ago by felipead6640 • updated 3 days ago by ATpoint26k
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HTSeq error about gene_id
... ##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 ...
htseq gene_id non-model written 21 days ago by felipead6640
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HTSeq pip installation in Ubuntu
... 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? ...
htseq ubuntu written 22 days ago by felipead6640 • updated 22 days ago by Mensur Dlakic2.5k
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Comment: C: wgcna annotation file for human data
... 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 felipead6640
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Comment: C: wgcna annotation file for human data
... 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 felipead6640
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Comment: C: wgcna annotation file for human data
... Could you tell me the steps on how to do this? ...
written 4 weeks ago by felipead6640
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wgcna annotation file for human data
... 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/ ...
wgcna modules annotation written 4 weeks ago by felipead6640 • updated 4 weeks ago by Kevin Blighe52k
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Linkage disequilibrium from multi-sample vcf file
... 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 ...
vcf snpeff vcftools ld written 6 months ago by felipead6640 • updated 6 months ago by RamRS25k
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fasta sequences from snpeff output file
... Is it possible to extract the fasta sequences of specific genes from a snpeff output (vcf) file? ...
fasta snpeff written 6 months ago by felipead6640

Latest awards to felipead66

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Bio-DB-HTS installation and ensembl-vep
Student 10 weeks ago, asked a question with at least 3 up-votes. For VariantFiltration warning "undefined variable"

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