User: williamsbrian5064

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Posts by williamsbrian5064

<prev • 27 results • page 1 of 3 • next >
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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 23 hours ago by williamsbrian506440
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Comment: C: Questions about Reference Sequence in DESeq2
... I just don't think mapping the RNA-seq reads to a Drosohpilia reference will tell me much about expression. I feel like I'm missing something here. ...
written 5 days ago by williamsbrian506440
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Comment: C: Questions about Reference Sequence in DESeq2
... Drosophila Melanogaster. I've looked at flybase but I'm not entirely sure what kind of file I'm looking for? They didn't explain much in the tutorial. ...
written 5 days ago by williamsbrian506440
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Questions about Reference Sequence in DESeq2
... I am trying to use Geneious to do some expression analysis using Dseq2. I was going through the tutorial and the reference sequence they used was super complete (NC_006841). It was annotated and it had the name of the proteins, min, max, length, and direction. I'm just wondering where they even got ...
assembly next-gen rna-seq sequencing written 6 days ago by williamsbrian506440 • updated 5 days ago by h.mon9.2k
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Comment: C: Is there a way to determine how related two samples are based off of WGS data
... That is correct, the PCA is just looking at SNPs. I guess I haven't tried removing breed specific SNP.. I honestly don't know how to do that. If you know of a way of doing that, I'd be interested. I generate every PCA plot possible when I run the data. You are right about the PC1 though. I'm really ...
written 6 days ago by williamsbrian506440
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Is there a way to determine how related two samples are based off of WGS data
... I'm currently working on a feline project. We are looking at breed specific mutations but have been running into some problems. In the past, we have been able to identify mutations that affect a particular breed. The thing is, cats don't care who they mate with and without supervision will mate with ...
genome next-gen sequence written 6 days ago by williamsbrian506440
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Comment: C: Trouble getting Cufflinks to run
... That is what I have heard. I have had success with HISAT2 and StringTie but I am wonder what to do with the data afterwards? I want to be able to do expression analysis ...
written 7 days ago by williamsbrian506440
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Comment: C: TopHat Error Qual length differs from seq length
... I tried their R script and got to step 9 and got blocked. They even have the troubleshooting sections that identifies the same error that I'm getting (The Ballgown function results in an error that the first column of pData does not match the names of the folders containing the ballgown data). I cou ...
written 7 days ago by williamsbrian506440
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Trouble getting Cufflinks to run
... I downloaded cufflinks but I can't seem to get it to work. The install instructions seem a bit out of date. I downloaded version 2.2 earlier and I'm having trouble getting the test_data to work. When I enter the command all I am getting is a solid grey box. Doesn't it look like it is running anythin ...
assembly rna-seq written 7 days ago by williamsbrian506440
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Comment: C: TopHat Error Qual length differs from seq length
... I tried the HISAT, StringTie, and Ballgown method today but I got a bit stuck at the R portion of it. I can't find much about the method really. I was wondering if you had any links? ...
written 7 days ago by williamsbrian506440

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