User: RMRG

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RMRG10
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Posts by RMRG

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Comment: C: tximport and de novo transcriptome
... Thanks! But could you direct me to the software I could use to actually do the summarization? I.E. to get 'genes' from transcripts in a similar way to what Trinity does for de novo assemblies? ...
written 12 months ago by RMRG10
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tximport and de novo transcriptome
... Hi, I typically run DE analyses through the trinity pipeline, but due to certain features of the transcriptome I'm currently working on, I've found it's essential to use a kmer value higher than allowed in trinity. I'm not used to the various software for doing DE analyses outside of trinity. I am ...
tximport salmon rna seq de novo written 12 months ago by RMRG10 • updated 12 months ago by James W. MacDonald51k
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Gene Set Enrichment based on gene presence/absence
... Hello, I've come across several gene set enrichment tools aimed at summarizing DE genes in RNA-seq datasets, but I have a slightly different goal, and I'm wondering if any of the available tools are suitable. I have several non-model organisms for which I've generated KEGG KO identifiers for. Inst ...
kegg gene set enrichment written 20 months ago by RMRG10 • updated 20 months ago by Lluís Revilla Sancho510
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Read normalization in a complex sample
... Hello, I am hoping for some help in understanding which read normalization approach is appropriate for the biologically complex samples that I'm hoping to do DE analysis on. I'm interested in DE of a bacterial endosymbiont of an insect; specifically, I'm trying to establish which genes are differe ...
normalization deseq2 differential expression written 2.2 years ago by RMRG10 • updated 2.2 years ago by Michael Love25k

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