User: Ana

gravatar for Ana
Ana20
Reputation:
20
Status:
New User
Location:
Portugal
Last seen:
3 years, 3 months ago
Joined:
3 years, 7 months ago
Email:
a*********@gmail.com

Posts by Ana

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Interpret Cufflinks output to detect novel isoforms
... I just have used cuffcompare (since I'm using an older version of cufflinks) and I was able to find some results! :D I just have to see if they are relevant or not by this time. Thanks for the help ! :) ...
written 3.4 years ago by Ana20
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Interpret Cufflinks output to detect novel isoforms
... Good evening, I followed the tuxedo protocol as described here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/pdf/nihms-366741.pdf . With the "normal" outputs that cufflinks provide (I'm searching on cuffdiff output files, but tell me if I'm wrong), how could I determine which of isoforms det ...
novel cufflinks isoforms rna-seq cuffdiff written 3.4 years ago by Ana20 • updated 17 months ago by jila-hessani0
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Comment: C: tophat-cufflinks command pipeline
... Yes, I did, but I was unable to find the .gtf file and also, at the beginning I thought it would be some specific kind of file other then the "normal" reference genome of human. Now I understood what it takes, thank you, and I'm sorry for my lack of knowledge at this point.  ...
written 3.4 years ago by Ana20
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Comment: C: tophat-cufflinks command pipeline
... For homo sapiens too. ...
written 3.4 years ago by Ana20
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Comment: C: tophat-cufflinks command pipeline
... I'm trying to accomplish the same task, but I'm new at this field, so, how do I get the refgene gtf file and the ucsc.hg19 reference genome?  ...
written 3.4 years ago by Ana20
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Comment: C: How to identify mitochrondrial genes in DNA?
... I currently have a directory with tophat output. As such I have a bam file and some bed ones with junctions, deletions and insertions.  ...
written 3.4 years ago by Ana20
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Comment: C: Identify aberrant splicing in DNA sequence
... Thanks for the help! Yes, what I'm thinking about is when an event of alternative splicing happens but then it generates some kind of mutation. So what you are saying is that I should search for differential splicing, is that it? Can you explain me or give me some links of what it consists on?  Abo ...
written 3.4 years ago by Ana20
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How to identify mitochrondrial genes in DNA?
... Hi everyone, Given a DNA sequence how to detect the mitochondrial genes? There's maybe some concepts of molecular biology that I'm not aware of, but I'm imagining that we have a full DNA sequence and in between it will result in different types of genes. I would like to know how I could find mitoch ...
gene mitochondrial written 3.4 years ago by Ana20 • updated 3.4 years ago by roy.granit740
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Identify aberrant splicing in DNA sequence
... Hi all, I'm really new in this stuff of bioinformatics and I'm having some trouble to understand how to do some things. Right now I have a DNA sequence that has already been aligned and everything. As far as I understood it has been used TopHat to do so, so it came with the other output files that ...
gene rna-seq alternative splicing written 3.4 years ago by Ana20 • updated 3.4 years ago by Devon Ryan85k
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Comment: C: Reference genomes repository
... Thanks for the answers. I probably didn't explained well before xD Anyway, i realized that ensembl and ucsc have reference genomes that I can download. But one thing that I can't understand is: when it says "biosamples" or "annotations" or "assembly" and then shows some files, what are they exactly? ...
written 3.6 years ago by Ana20

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