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OMA - How to retrieve orthologs of only one representative of each taxonomy rank?

oma orthologs orthologs oma written 4 months ago by anusblat • 0 • updated 4 months ago by Christophe Dessimoz • 500

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How export HOG viewer tree with orthologs in OMA

oma orthologs oma ortholog written 4 months ago by anusblat • 0 • updated 4 months ago by Christophe Dessimoz • 500

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Recent Replies

C: Analysis Without Replicates by ATpoint ♦ 10k
In case the shrinkage does not give satisfying results and you have to use unshrunken FCs, I woul...
C: RNA-strandness of single cell library prep methods by Juke-34 • 1.7k
I guess yes firststrand (RF) sound the one to use.
C: GATK best practices for Broad-produced NGS data by Mehulsharma.253 • 0
Thank you ! GATK forums seems to be having some issues with enabling posting and commenting becau...
C: Analysis Without Replicates by kristoffer.vittingseerup • 980
Sounds like a good plan, especially with the log2FC shrinkage - just remember log2FC != pvalues
A: Could you please tell me how should I analyze the difference between KO and WT m by kristoffer.vittingseerup • 980
I highly recomend Seurat to do the analysis downstream of quantification - it is easy to use, fas...
C: GATK best practices for Broad-produced NGS data by WouterDeCoster ♦ 35k
I think the GATK forum would be a more appropriate place for this question, but I have asked some...
A: Extracting the full read ID when converting from BAM -> FASTQ by toralmanvar • 710
You can replace space in header with "_" in both R1 and R2 reads file. Assuming second segment is...
A: Genotypes from different strand for same variant position by finswimmer ♦ 7.8k
Describing a variant on a different strand is always confusing. If you are just talking about th...
A: Failed to populate reference for id 1? by cmdcolin • 930
Following advice from @finswimmer, I modified the BAM header and deleted all other chromosomes ex...
C: Failed to populate reference for id 1? by cmdcolin • 930
Thank you very much for this information, that worked! Do you happen to have a source for this in...
C: Failed to populate reference for id 1? by finswimmer ♦ 7.8k
Ok, I took a closer look at this. In your reference file must be all sequence names listed in th...
C: Cell density as a function of cortical depth by RamRS ♦ 19k
Please see https://www.biostars.org/p/309884/ to add your images properly. You need **the direct ...

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