User: Biok

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Biok0
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Posts by Biok

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Best software to visualize a phylogenetic tree coupled to the presence/absence p
... Thank you for the recommendation! I will try iTOL. ...
written 5 weeks ago by Biok0
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Best software to visualize a phylogenetic tree coupled to the presence/absence pattern of clusters of orthologous proteins (COGs)
... Hi everyone, I am looking for a good comparative genomic tool or R package where it is possible to have a phylogenetic tree on one side and the distribution of COGs across the species on the other. Do you know of a program for this? Thank you! ...
genome R sequence assembly written 5 weeks ago by Biok0
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How to extract reads from a particular gene from a metagenome
... Hi everyone, I have a very basic question, I have metagenomic samples and I want to extract reads from a particular gene (amoA gene) to see the diversity of this gene between samples but I am not sure what would be the best approach. Should I just blast the metagenomic reads against amoA sequences? ...
gene assembly next-gen sequence written 7 weeks ago by Biok0
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Short contigs after megahit assembly of metagenomic samples
... Hi everyone, I am working with metagenomic samples and I co-assembled the two metagenomic samples with megahit, the problem is that I got a lot of less than 1000 bp contigs that I had to remove because my goal is to reconstruct metagenome-assembled genomes. But by doing this, I lost a lost 93% of c ...
assembly next-gen sequence written 10 weeks ago by Biok0 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: Low value of mapped reads against a metagenomic co-assembly
... thanks for the reply, I selected contigs larger than 1000 bp because my goal is to reconstruct Metagenome-assembled genomes (MAG's). Initially I got around 7,000,000 contigs from Megahit but after selecting contigs larger than 1000 bps I only got an final assembly of around 455,000 contigs and I use ...
written 3 months ago by Biok0
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Low value of mapped reads against a metagenomic co-assembly
... Hi, everyone, I have two metagenomic samples, I co-assembled these samples together using both spades and Megahit and then I mapped each sample against the co-assembly using bowtie2. I got for each sample around 40 % overall alignment rate. I would like to know if this low value is normal (given tha ...
assembly next-gen alignment written 3 months ago by Biok0 • updated 3 months ago by biobiu110

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