User: james.lloyd

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james.lloyd80
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United States
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http://pmb.berkeley.ed...
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@JamesPBLloyd
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1 year, 1 month ago
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4 years, 2 months ago
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j**********@berkeley.edu

New to computational biology, the command line, and programming in Python (and the Oxford comma). Trying to get my head around the tools out there and how to use programming to get an answer from my data. Please take pity on this noob. 

Posts by james.lloyd

<prev • 45 results • page 1 of 5 • next >
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Repeat masked GFF3 not being converted to GTF
... I am trying to convert the GFF3 file of the version 3.3 of the moss (Physcomitrella patens) genome into a GTF file with: gffread my.gff3 -T -o my.gtf This worked fine when I was converting the gene GFF3 to GTF (Ppatens_318_v3.3.gene_exons.gff3). The error I am getting with the repeatmasked version i ...
gtf gff3 gff cufflinks written 13 months ago by james.lloyd80
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Comment: C: Is Sleuth a good package?
... In addition to it being published as a "pre-print" in the bioRxiv, as igor pointed out, it is a useful and powerful piece of software. It is the only package (to my knowledge) that can take advantage of the bootstrapping that kallisto and salmon both do. This is one of the main selling points of t ...
written 23 months ago by james.lloyd80
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What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
... Hello Internet, So I have an issue where I have more than one treatment. Treatment A, Treatment B, Treatment C and Treatment D (for example). I want to use kallisto or salmon to quant the transcripts and then use Sleuth to find differential transcripts. But I do not understand the commands very we ...
sleuth salmon kallisto rna-seq dte written 23 months ago by james.lloyd80 • updated 26 days ago by lalvarez10
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ggplot histogram normalize the tallest bin to 1 and adjust all others accordingly?
... I have multiple samples (types) and I want to plot there values on the same histogram. I can do this but because the groups are very different in the number in each type, I think the very different heights of the bars could hiding a small difference between the groups. So I wanted to change the plot ...
R ggplot plots histogram written 2.1 years ago by james.lloyd80 • updated 2.1 years ago by Selenocysteine510
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Comment: C: What does Ensembl/Genecode gene_type "processed_gene" really mean?
... Thanks but these are not for pseudogenes. They have a different gene_type in the databases which I understand the distinction. ...
written 2.2 years ago by james.lloyd80
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Comment: C: Looking for changes in expression of transposable elements in human cells
... Thanks, that looks interesting. PDF downloaded! ...
written 2.2 years ago by james.lloyd80
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Looking for changes in expression of transposable elements in human cells
... I have some RNA-seq datasets from human cells and I am interested to see if the expression of transposable elements (TEs) change in different treatments. I found this easy to do with the plant Arabidopsis thaliana as the TAIR10 annotation of the genome has gene types that are TEs. However, such a ge ...
transposable elements expression rna-seq written 2.2 years ago by james.lloyd80
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What does Ensembl/Genecode gene_type "processed_gene" really mean?
... I am using the gencode.v19.annotation.gtf (head of the GTF below) to assign gene_types to the transcripts in my study via ensembl gene IDs. And example line from the GTF is also below. Some gene_types have the name processed_transcript while other are lincRNA or antisense etc. Ensembl just list ...
annotation rna-seq ensembl written 2.2 years ago by james.lloyd80 • updated 2.1 years ago by i.sudbery2.8k
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Comment: C: RNA-Seq analysis for individual genes
... Sorry for not responding sooner. As I understand it, bootstrapping is when a subset of the data (reads) are analysed to estimate the technical variation in quantification level. You can read more in Lior Pachter's blog here https://liorpachter.wordpress.com/2015/05/10/near-optimal-rna-seq-quantific ...
written 2.2 years ago by james.lloyd80
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Comment: C: RNA-Seq analysis for individual genes
... I have not personally used RSEM so I cannot comment on what is best to do with that output. I am not sure it can be used as input into Cufflinks. These can probably be inputted into something like DESeq2 or EdgeR but I have never done that analysis. This raises another variation in tools for RNA-s ...
written 2.4 years ago by james.lloyd80

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Popular Question 23 months ago, created a question with more than 1,000 views. For In ggplot, assign a variable/category to a specific color?
Popular Question 23 months ago, created a question with more than 1,000 views. For Annotate transcript isoforms from Cufflinks GTF with splicing types
Popular Question 23 months ago, created a question with more than 1,000 views. For Can you add a label key to heatscatter plot in R?
Popular Question 23 months ago, created a question with more than 1,000 views. For Convert TAIR IDs to NCBI IDs for Gorilla
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: In ggplot, assign a variable/category to a specific color?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Can you add a label key to heatscatter plot in R?
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