User: williamsbrian5064

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Posts by williamsbrian5064

<prev • 36 results • page 1 of 4 • next >
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StringTie Error regarding GFT file
... Hi, I am working on some RNA seq data. A colleague of mind inserted a human gene into the Drosophila genome. I'm trying to figure out how to add the gene to the fasta file and the gtf file so I can see the expression of the gene. Do anyone know how to do that? I attempted to add the gene to the fas ...
software error assembly next-gen rna-seq written 20 hours ago by williamsbrian506440
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Comment: C: Stringtie error with gtf file
... Maybe I need to build my own index? ...
written 29 days ago by williamsbrian506440
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Comment: C: Stringtie error with gtf file
... I believe a similar version. Do you think that is the issue? ...
written 29 days ago by williamsbrian506440
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Stringtie error with gtf file
... Hi! I am getting this error when I try to run stringtie on some RNA-seq data. This is what I am getting. WARNING: no reference transcripts were found for the genomic sequences where reads were mapped! Please make sure the -G annotation file uses the same naming convention for the genome s ...
software error next-gen rna-seq written 4 weeks ago by williamsbrian506440
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Any easy was to run a differential expression analysis?
... I need some help with some RNA-seq data. All I want to do is a differential expression analysis but I'm struggling. Does anyone know of a simple up to date method to do this analysis? I tried using kallisto followed by Deseq2 but I can figure out how to get Deseq2 to work in R. I got Sleuth to work ...
R rna-seq written 7 weeks ago by williamsbrian506440
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Does Anyone understand the Sleuth Shiny app used to visualize your RNA-seq Data??
... I was wondering if anyone knew how to interpret the Sleuth RNA-seq data? The column names are "pval", "qval", "rss", "sigma_sq", "tech_var", "mean_obs", "var_obs", "sigma_sq_pmax", "smooth_sigma_sq", and "final_sigma_sq". My goal with sleuth was to do a differential expression analysis but I can't f ...
R next-gen rna-seq written 7 weeks ago by williamsbrian506440 • updated 7 weeks ago by h.mon11k
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Comment: C: How to find an inserted human gene in Drosophila RNA-seq data
... I will give that a try! Thanks for the help ...
written 11 weeks ago by williamsbrian506440
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Comment: C: How to find an inserted human gene in Drosophila RNA-seq data
... How would I go about doing that? I'm not sure how to alter the transcript fasta file to do that? ...
written 11 weeks ago by williamsbrian506440
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How to find an inserted human gene in Drosophila RNA-seq data
... I am working on a collaboration and we recently generated some RNA-seq data. So the lab that we are working with inserted a human gene into the Drosophila genome to see the effects of a specific mutation. They were able to insert the gene and did some RNA sequencing. I was given the task of working ...
genome assembly rna-seq sequencing written 11 weeks ago by williamsbrian506440
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Sleuth_fit error "`Error in if (sum(valid) == 0) { : missing value where TRUE/FALSE needed"
... Hi, I am using Sleuth to generate some RNA-seq data. I keep getting this error when I try to run the program and I was hoping someone will be able to help me. When I try and run the `so <- sleuth_fit(so, ~condition, 'full')` I keep getting this error `Error in if (sum(valid) == 0) { : missing va ...
software error R rna-seq assembly written 3 months ago by williamsbrian506440

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