User: dark.lord

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dark.lord0
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Posts by dark.lord

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Comment: C: Recent metatranscriptomics workflow
... Downloaded R and am following some crash course to refresh the few skills acquired in my BSc. :D Anything else to add besides this funny meme? ...
written 5 months ago by dark.lord0
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Recent metatranscriptomics workflow
... Hi guys, I am starting to work with metatranscriptomics data and I don't know where to turn. A short recap: I have 3 annotated bacterial genomes. I have 6 metatranscriptomes I have to map against them. What I aim to: 1) know the expression of each genes in each genome; 2) compare the expressio ...
metatranscriptomics workflow kallisto written 5 months ago by dark.lord0
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Comment: A: Getting average fragment length for single end reads
... Is it wrong to use the one-liner provided here to calculate average fragment size and sd? https://www.biostars.org/p/243552/ ...
written 6 months ago by dark.lord0
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Comment: C: Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
... Thanks again for your answer - what you say is indeed right; but when the 16S shows >98-99% similarity, I expect the genomes to have ANI values above 94. I cannot figure out how two populations which have quasi-identical 16S (1511/1533 nucleotides matching, 99%) return ANI values of 80. That's wh ...
written 7 months ago by dark.lord0
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Comment: C: Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
... Thanks for your answer - I didn't use that CheckM function yet, but I guess it works like rnammer? Also, I didn't do any analysis on other marker genes and that would be a nice idea, but still it won't help justifying the identical 16S content in two different subpopulation. ...
written 7 months ago by dark.lord0
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Comment: C: Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
... Thanks for your answer - I linked the wrong rep (fixed) but I looked into the right one :D good to know about the length. I actually end up in your 'good luck with this one' case, as I have 2x300 bp Illumina. For the genome reconstruction, the pipeline was: assembly with metaSPAdes binning with ...
written 7 months ago by dark.lord0
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Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
... Hi all, A short background: I have 4 metagenomes. In all of them, two very closely-related populations of the same bacterial cluster co-occur. I obtained 4 final bins, and according to ANI value, I have two different genomes (ANI around 80). The point is, when I extract the rRNA genes from the b ...
assembly 16s rrna spades reago written 7 months ago by dark.lord0
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Comment: C: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
... Nice one mate! This works like a charm. ...
written 7 months ago by dark.lord0
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Answer: A: The --contig option for SPAdes
... My understanding of this is that the contigs are used as a backbone for assembly. Using these scaffolds/contigs as a backbone, the assembly becomes more of a mapping - the raw (trimmed) reads stretch the contigs, and that's how it helps with gap closure. The same thing could happen with the mapping ...
written 7 months ago by dark.lord0
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Comment: C: Metawatt [ERROR] String out of range in Six frame Pfam module
... Thanks for the reminder, done both. ...
written 8 months ago by dark.lord0

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