User: williamsbrian5064

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Posts by williamsbrian5064

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Comment: C: How would you trim this RNA-seq data
... When you say adapters, are you referring to the "Overrepresented sequences"? or the actual "Adapter content"? Also, why do you think there are single end adaptors? This was a paired end? ...
written 11 days ago by williamsbrian5064100
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How would you trim this RNA-seq data
... Hi, I am working on an RNA-Seq project. We just got back some sequencing and I had a couple questions about it. I figure someone here might be able to help me out a bit. So I think the sequencing doesn't look too bad. I don't really like trimming RNA-seq data if I don't have to, but I attached i ...
next-gen rna-seq written 11 days ago by williamsbrian5064100
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How to edit ped and map files
... Hi, I just had a quick question. I was wondering if there was an easy way to manipulate ped and map files? Maybe in R? I specifically need to edit my map file. I am having an issue with the marker ID (rs# or snp identifier). I need to add them into the files and I'm not sure how to do this. Is the ...
R chip-seq plink snp assembly written 14 days ago by williamsbrian5064100
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How to add gene symbol to RNA-Seq data using R
... Hi, So I am trying to add the gene ID to my RNA-Seq data. So what I did was use Salmon to quantify my reads but instead of doing some DE analysis, I want to try and us an alternative program to try and do a little machine learning. So I really just need add the gene symbol next to the transcript ID ...
R rna-seq written 10 weeks ago by williamsbrian5064100 • updated 10 weeks ago by RamRS19k
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Comment: C: How to change conditions in DESeq2
... Kevin! You're the man! Sorry for the late response, I was trying to get your second option to work. I really appreciate your response! I was able to get both of your options to work. I had to play with what you wrote a bit. I had to run the following to get the data in the right order MyData ...
written 3 months ago by williamsbrian5064100
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How to change conditions in DESeq2
... Hi, I am kind of new to R so I apologize if I don't give all the info that is need. I will keep and eye on this post and add any additional info that is requested. So I have two conditions in my dataset, fed and starved. The "fed" samples are my controls and the "starved" samples are my affected. S ...
R rna-seq written 3 months ago by williamsbrian5064100 • updated 3 months ago by Kevin Blighe32k
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Comment: C: DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' mu
... Amazing! Both of those worked like a charm. I apologize, I didn't realize I forgot to add a couple lines of regarding `[select,]` but you figured it out. I was able to mesh the two so the plots aren't massive. Thanks so much for taking the time to help me! I really really appreciate the help Kevin! ...
written 3 months ago by williamsbrian5064100
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Comment: C: DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' mu
... I was really thrown off by that as well. It took me awhile how to figure out how to change the rownames in dds ...
written 3 months ago by williamsbrian5064100
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DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
... Hi, I am attempting to make some heat maps with some RNA-Seq data. I used Salmon for my quantification and followed [this][1] link to import my data into R so I can use Deseq2. So I am just going through the Deseq2 little tutorial [here][2]. I am trying to follow their instruction on how to create ...
software error R rna-seq written 3 months ago by williamsbrian5064100
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Comment: C: Issue with Samtools variant calling
... I am using version 1.8 ...
written 4 months ago by williamsbrian5064100

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Best way to merge multiple VCF files
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Best way to merge multiple VCF files
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