User: jfo

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jfo0
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Posts by jfo

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Comment: C: Genbank GI accession format for DAVID input
... I have the Official Gene Symbols, which actually works. My confusion comes from the use of the unigenes with nr hits but with no gene symbols. Should I just proceed with those which had gene symbols? This is why I was looking for a way to get all these unigenes with nr hits to have other accession n ...
written 1 hour ago by jfo0
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Comment: C: Genbank GI accession format for DAVID input
... Thank you for the prompt answer. I do have the accessions; however, I am not sure how to use different input types for the analysis in DAVID. For example I have ref (mostly XP_), dbj, gb, or sp for the accessions. How do I convert these accession IDs to a DAVID-"interpret-able" format? I am having ...
written 18 hours ago by jfo0
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Genbank GI accession format for DAVID input
... Hi! I would like to seek an advice or two with regard to the proper format of GENBANK_GI_ACCESSION for DAVID Function Analysis. I tried these formats: 1. gi123456 2. gi|123456 3. 123456 Sadly, nothing worked. I could not find any examples. I prefer gi accessions for this because all my unigenes o ...
david functional analysis written 20 hours ago by jfo0 • updated 19 hours ago by Istvan Albert ♦♦ 79k
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Answer: A: Any web server for KOG annotation for denovo transcriptome assembly?
... You can upload your pep files [here][1]. Then graph the results using the R code [here][2]. [1]: http://%20http://weizhong-lab.ucsd.edu/webMGA/server/kog/ [2]: https://stackoverflow.com/questions/39613006/how-to-add-main-title-and-manipulating-axis-labels-in-ggplot2-in-rstudio?noredirect=1&am ...
written 4 weeks ago by jfo0
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Answer: A: calculating allele frequency difference or Fst value ?
... Hello Seta, [Here][1] are some quick answers to your questions. You can always try both methods to determine genetic differences in your populations of interest. Which method is more appropriate will depend on the hypotheses you want to test. For estimating genetic differentiation between populati ...
written 10 weeks ago by jfo0
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Comment: C: Changing Quality Scores Within Bam Files
... "usage (converts fastq 1.3/1.5 to sanger): samtools view -h in.bam | bam_rescale_quals.py - | samtools view -bS - > out.bam" So I guess, yea. ...
written 2.2 years ago by jfo0
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Computing Fst in multiple population using Popoolation2
... Dear everyone, I have a RNA-seq data for three populations: pooled individuals with at least n = 40 per library; two libraries each population (a total of 6 lib); around 40M PE reads per library). Objective: Get highest ranking SNPs using their Fst values to be used for SNP genotyping and pop gen ...
popoolation2 fst rna-seq written 2.3 years ago by jfo0
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Comment: C: Error in running "diffExpressedVariants" function in kissDE R package
... Hi @vincent.lacroix, I also encountered an almost similar error: "Error in .validate_assayDataElementReplace(obj, value): object and replacement value have different dimensions\n An error occured, unable to fit models on data." This actually occured when I ran KissDE using my data; however, this ...
written 2.3 years ago by jfo0
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Comment: C: Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)
... Hi microfuge! Thanks for the reply! Do you happen to know a software that can compute for hudson's Fst per SNP? Thanks again! ...
written 2.5 years ago by jfo0
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Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)
... Hello everyone, I used CRISP to call SNPs from a transcriptome data, which was a result of pooled sampling (we have to pool 10 - 60 juveniles per library to get an amenable amount of RNA). I have 3 populations with 2 libraries each. Now, I would like to compute for the Fst for individual SNPs and ...
transcriptomics snp written 2.5 years ago by jfo0

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Compute for individual Fst of SNPs from a transcriptomic data (pooled samples)

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