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User: rmf

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rmf • 70
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Posts by rmf

<prev • 38 results • page 1 of 4 • next >
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Picking differentially expressed genes using consensus
... Differential gene expression can obviously be run using various programs and workflows (I call methods from here on). And each method may not necessarily give the same list of DE genes. Would it make sense to pick DE genes as an intersect from various methods and use them a final list of DE genes? O ...
rna-seq differential gene expression written 8 weeks ago by rmf • 70
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Downstream applications of Differential transcript expression
... I am looking for examples of possible downstream applications/methods for Differential transcript expression. For genes, I would go for enrichment analysis, GO analysis, pathway analysis etc. I have a list of differentially expressed transcripts. What then? ...
rna-seq written 8 weeks ago by rmf • 70 • updated 8 weeks ago by theobroma22 • 910
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Working with PVCA
... I have my RNASeq counts and the various factors of my experimental setup (condition,strain,pool etc). I am interested to know which of these effects matter and how much so that I can make a decision of how to model them in GLM. I have found this package called `PVCA` which seems to show the proport ...
pvca rna-seq dge written 5 months ago by rmf • 70
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Comment: C: Transcriptome length of organisms
... I was hoping this information would be available on one of the standard databases or websites rather than me having to do this for every organism. But thanks anyhow. ...
written 10 months ago by rmf • 70
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Comment: C: Transcriptome length of organisms
... Yes. I suppose the transcriptome length is the the sum of all RNA coding sequence. I agree that adding up all splice variants don't make sense. Perhaps the longest transcript may not be optimal either. Instead, I would go for the length of a union of all variants from a gene. @Prasad I have come acr ...
written 10 months ago by rmf • 70
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Transcriptome length of organisms
... Where can I find the transcriptome length for various organisms? Or at least the common model organisms? If I go to the ensembl page for example, [fruitfly][1], The transcriptome length is not indicated. [1]: http://www.ensembl.org/Drosophila_melanogaster/Info/Annotation ...
rna-seq written 10 months ago by rmf • 70
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Comment: C: bowtie2-build cannot use multiple cores
... Of course.. versions! Apologies for accusing the documentation. I was quite frustrated with the tuxedo suite in general. Anyhow, thanks for the explanation :-) ...
written 10 months ago by rmf • 70
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Answer: A: bowtie2-build cannot use multiple cores
... I think I have figured it out. It's probably a case of rubbish documentation. The switch for multi-cores seems to be `-p`. Yet, this does not work for me bowtie2-build \ -p 2 \ "$path_genome" \ "$path_index" but this does work: bowtie2-build -p 2 "$path_genome" "$path_index" ...
written 10 months ago by rmf • 70
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bowtie2-build cannot use multiple cores
... I tried running `bowtie2-build` as below bowtie2-build \ --threads 8 \ "$path_genome" \ "$path_index" and it gives the following error that `threads` is not defined. Bowtie2 indexing genome bowtie2-build: unrecognized option '--threads' Bowtie 2 version 2.2.6 by Ben ...
bowtie2 written 10 months ago by rmf • 70
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Comment: C: Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
... Is it possible to use this without the GUI? ...
written 10 months ago by rmf • 70

Latest awards to rmf

Popular Question 14 days ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Design matrix not of full rank.
Popular Question 10 months ago, created a question with more than 1,000 views. For RNA Seq: GC Content extra peak
Student 10 months ago, asked a question with at least 3 up-votes. For Consequences of degraded DNA for Sequencing
Scholar 10 months ago, created an answer that has been accepted. For A: bowtie2-build cannot use multiple cores
Supporter 16 months ago, voted at least 25 times.
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