User: Ace

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Ace10
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Posts by Ace

<prev • 7 results • page 1 of 1 • next >
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Comment: C: RATT annotation transfer tool usage.
... A tutorial would be fantastic. I'm struggling with this program, currently. ...
written 9 weeks ago by Ace10
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Comment: C: Replacement for Tribe-MCL?
... I would be willing to try any clustering program with a good track record of retrieving gene families which may contain repetitive sequences. Ease of use would be an additional factor I would consider. ...
written 10 weeks ago by Ace10
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Replacement for Tribe-MCL?
... I am looking to find gene families from transcriptome and genome data. Tribe-MCL seems to no longer be available, does anyone know what has replaced it? Sorry if this is a silly question. ...
tribemcl mcl gene families rna-seq written 10 weeks ago by Ace10
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Comment: C: ENA bulk download all fastq files in study
... It seems as though your project is actually a "Parent project" with many components. So, while you can get texts for them individually, but not all at once. I don't have an exact fix but in my experimenting with wget while trying to familiarize myself with FTP I have a makeshift answer that may work ...
written 11 months ago by Ace10
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Comment: C: #rna-seq 2 tissue, 2 different individual, no replicate, what can i analysis?
... I suppose with any high-enough coverage/quality RNA-seq sample you can look to do transcriptome assembly and isoform discovery but if you're in a model organism that's still not very novel, so again would only be good for practice. Even in bioinformatics work, your time is best spent if you know wha ...
written 14 months ago by Ace10
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Answer: A: #rna-seq 2 tissue, 2 different individual, no replicate, what can i analysis?
... DeSeq (not DeSeq2) can do differential analysis without replicates. You could choose to look at the different tissues, making the assumption your individuals are similar enough to draw some conclusions about the population. This would be a very dirty analysis, but it might make good practice for a b ...
written 14 months ago by Ace10
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Comment: A: direct two-color Agilent SAM analysis?
... Did you ever find a solution to this? I also found difficulty converting the limma data into an expression set, it doesn't seem capable of understanding the two channels as control and treatment. I think agilent documentation has been largely overlooked for this program. ...
written 15 months ago by Ace10

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