User: samche42

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samche420
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Posts by samche42

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How to export KEGG presence absence data from BRITE output?
... Hi I've used a combination of BlastKoala and KEGG to find the presence and absence of genes in three related Burkholderia strains. I used the "Reconstruct Brite" option and 'viewed K00001". The resultant hierarchical list is exactly what I need as the presence/absence of each gene is indicated by ...
brite data export kegg written 10 months ago by samche420 • updated 8 months ago by Biostar ♦♦ 20
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R: apex Multigene alignment problems "DNA sequences in list not of the same length"
... Hi! I'm trying to create a single phylogenetic tree from a concatenation of 10 000 individual gene alignments. I used OMA to find 10 000 orthologous genes from 23 bacterial genomes. I then used muscle to align sequences in multifasta files of each orthologous gene set using the following: > mu ...
apex R astral species tree multigene alignment written 11 months ago by samche420
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Comment: C: Clarification of OMA tree metrics
... Thank you!! i really appreciate the help :) ...
written 11 months ago by samche420
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Clarification of OMA tree metrics
... Hi! I've used OMA 2.2.0 standalone to generate an estimated species tree from 34 genomes. The tree was successfully generated but I can't seem to find any explanations for the numbers on the tree. Are the node numbers the bootstrap values? Levels of similarity? And the scale bar? Is that a reflecti ...
orthologs oma species tree written 11 months ago by samche420 • updated 3 months ago by Biostar ♦♦ 20
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Can't submit uploaded sequence data on MG-RAST
... Hi there I've successfully uploaded my metadata file and assembled, shotgun metagenomic dataet to my MG-RAST inbox. The metadata passed the QC-like step, my sequwnce data uploaded just fine and I could happily move on to the submission step. Everything works beautifully until I get to the tab where ...
mg-rast upload shotgun metagenome sequencing written 22 months ago by samche420 • updated 18 months ago by himanshu.genetics0

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Popular Question 7 months ago, created a question with more than 1,000 views. For Can't submit uploaded sequence data on MG-RAST

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