User: BioBing

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BioBing80
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Posts by BioBing

<prev • 40 results • page 1 of 4 • next >
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Contig cutoff of 300 bp - why? (Trinity transcriptome assembly)
... Hi all, This may be a stupid question, but I am curious to find out why exactly many papers chose a contig cutoff of 300 bp when performing a Trinity de novo transcriptome assembly. In my head, it makes sense since short contigs probably do not provide a lot of information and are just "contamina ...
trinity contigs rna-seq assembly written 11 weeks ago by BioBing80 • updated 9 weeks ago by jwhan.algae0
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Comment: C: DAVID gene enrichment - multiple Entrez IDs per gene symbol, what to do?
... Hi Jean-Karim, Thank you for your response! There is no reference genome available for the species I am working with, that is why I am using a Trinotate annotated gene list as background. But yes, the redundancy in the gene conversion makes it troublesome. Best, Birgitte ...
written 3 months ago by BioBing80
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DAVID gene enrichment - multiple Entrez IDs per gene symbol, what to do?
... Hi all, I need your help since I am very much in doubt about the right approach for gene enrichment analysis. For my non-model organism, I have a background list of official gene IDs (originating from a Trinotate annotated de novo transcriptome, which also assigned GO-terms to each gene) and a lis ...
gene-enrichment david go written 3 months ago by BioBing80
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Comment: C: How to split columns into rows based on gene ids in R?
... If it is not too much trouble, I would love to see an example :-) Thank you! ...
written 5 months ago by BioBing80
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Comment: C: How to split columns into rows based on gene ids in R?
... Thank you, I am new to all this "programming stuff" - learning every day :-) I tried your code, but I cannot get it to work for some reason - it returns a list of the "Gene" names without the GO_terms in the terminal, but the txt file still looks the same. But I will definitely read up on awk and ...
written 5 months ago by BioBing80
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Comment: C: How to split columns into rows based on gene ids in R?
... It works :-) It is slow, but it works! Thank you so much ...
written 5 months ago by BioBing80
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Comment: C: How to split columns into rows based on gene ids in R?
... Because I have to use the "transformed" data in R, so I thought there had to be a smart way to do this. I was not aware that Python/awk etc. is better for text formatting until now. I am still pretty new to all of this "programming stuff" - learning every day :-) ...
written 5 months ago by BioBing80
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How to split columns into rows based on gene ids in R?
... Hi all, Does any of you cool R-sharks know how to transform data from this: Gene GO_terms ENO GO:0000015^GO:0000287^GO:0004634^GO:0006096 CCYL1 GO:0000079 SAP30 GO:0000118^GO:0003677^GO:0004407^GO:0046872^GO:0006351 To this in R?: Gene GO_terms ENO GO:00000 ...
R written 5 months ago by BioBing80 • updated 5 months ago by st.ph.n2.1k
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Comment: C: Looking for recommendations of R package for GO enrichment analysis based on gen
... Thanks! I will check it out! ...
written 5 months ago by BioBing80
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Looking for recommendations of R package for GO enrichment analysis based on gene list and a Trinotate report
... Hi all, I was wondering if some of you could recommend me a good R package for GO Enrichment Analysis and creating graphs of functional gene clusters? The data I want to use in the analysis: 1) A Trinotate annotation report that includes GO-ids/terms for each annotated gene 2) A list of genes t ...
R trinotate rna-seq go written 5 months ago by BioBing80 • updated 5 months ago by Satyajeet Khare1.2k

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