User: dark.lord

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dark.lord0
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Posts by dark.lord

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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 23 days 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 weeks 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 weeks 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 weeks 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 weeks 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 8 weeks 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 8 weeks 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 11 weeks ago by dark.lord0
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Comment: C: Metawatt [ERROR] String out of range in Six frame Pfam module
... Already checked with a couple of one liners found on this thread: https://www.biostars.org/p/78786/ There are no empty sequences. ...
written 11 weeks ago by dark.lord0
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Metawatt [ERROR] String out of range in Six frame Pfam module
... Hi all, I get this error when running the Six frame Pfam module: Metawatt [INFO|2:07:40] Running "Six frame Pfam"... Metawatt [INFO|2:07:40] Set HMM evalue [1.0E-10] Metawatt [INFO|2:07:40] Set processors used [30] Metawatt [INFO|2:07:40] Set mimimum length for HMM profile hits [5 ...
assembly binning metawatt written 11 weeks ago by dark.lord0 • updated 11 weeks ago by Pierre Lindenbaum108k

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