User: nash.claire

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nash.claire330
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Canada
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6 months, 2 weeks ago
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Posts by nash.claire

<prev • 72 results • page 1 of 8 • next >
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Answer: A: Get a list of human genes that are known to have introns within the 5'UTR
... Just to add, if using Pierre's script above, I added an additional step to only pull out the transcripts that have a protein coding biotype. This is easily done using Biomart in R. ...
written 2.1 years ago by nash.claire330
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Comment: C: Get a list of human genes that are known to have introns within the 5'UTR
... Hahaha if this leads to a paper in any way I'll be surprised! But noted!! ...
written 2.2 years ago by nash.claire330
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Comment: C: Get a list of human genes that are known to have introns within the 5'UTR
... Sorry it's been a long day. Next time I'll do it right. ...
written 2.2 years ago by nash.claire330
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Answer: A: Get a list of human genes that are known to have introns within the 5'UTR
... Wow that's awesome it worked beautifully. Thanks Pierre! ...
written 2.2 years ago by nash.claire330
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Get a list of human genes that are known to have introns within the 5'UTR
... Hi all, I wondered if anyone knows of a way to take all the genes in the human genome and pull out all of those that feature introns within the 5'UTRs?? Here is an example of the type of gene/transcript that I'm talking about (although this link is for the hg19 genome build) http://grch37.ensembl. ...
genome gene sequence written 2.2 years ago by nash.claire330
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Comment: C: Running EvidentialGene with both genome-guided and de novo assemblies
... Hi Don, Thank you for getting back to me. I am sold on the algorithm for sure. It looks like it is really useful and does exactly what I'm looking for. The problem I'm having is figuring out how to use the tool on the terminal. What commands do I need to use and in what order? I should probably m ...
written 2.4 years ago by nash.claire330
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Running EvidentialGene with both genome-guided and de novo assemblies
... Hi, I was hoping to get some help on how to run EvidentialGene with multiple transcript assemblies generated from both genome-guided and de novo assembly tools. I have read posts on here and papers that refer to EvidentialGene but these are generally referring to assmeblies with no known genome. ...
assembly rna-seq written 2.4 years ago by nash.claire330 • updated 2.4 years ago by gilbert.bionet130
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Comment: C: Clarification of good pipeline for transcriptome assembly of RNA-seq data
... Hi Amitm, So you hit the nail on the head. There was a lack of communication in our lab. I thought that my reads had been aligned (by my colleague) with Subread using the "subjunc" function. Turns out it hadn't and therefore didn't have exon junction info. Once aligned properly and checked as you s ...
written 2.4 years ago by nash.claire330
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Comment: C: Clarification of good pipeline for transcriptome assembly of RNA-seq data
... Hi Tiago, Thank you for the reply. I took a look at the paper you referenced but it seems to be a little vague/skim over the bit that I'm most interested in. There also seems to be a lot of emphasis on Cufflinks in there. I'm actually at this stage not too concerned about the quantification of the ...
written 2.4 years ago by nash.claire330
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Comment: C: Clarification of good pipeline for transcriptome assembly of RNA-seq data
... Hi Amitm, Thank you for the reply. Do you have any experience using the newer version of Stringtie? It's just I seem to have used exactly the same parameters/commands as you and it gives me that output you see in the image above. I don't know why I'm not getting results like you have shown. I'm con ...
written 2.4 years ago by nash.claire330

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