User: dark.lord

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dark.lord30
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Posts by dark.lord

<prev • 21 results • page 1 of 3 • next >
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Is there a way to place short reads within MEGA software?
... Dear community, In brief, what I would like to do is to place several short sequences on a pre-existing tree topology. I know I can achieve this through pplacer using a RAxML-made tree, but I was wondering whether there is a way to do it within the MEGA suite (I am using version 10 - X), as I bu ...
phylogenetics mega short reads pplacer written 11 weeks ago by dark.lord30
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Comment: C: How do I decide the mapping quality score in featureCounts?
... Thanks @genomax. I think I will go with Q = 0, also because I made trimming and bbmap'd with minid=1, so reads in the SAM file should have already a good quality. Read the blog and makes me wonder, why are there so few instances of standardisation in bioinformatics? :( ...
written 3 months ago by dark.lord30
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How do I decide the mapping quality score in featureCounts?
... Hey guys, I noticed that with featureCounts the -Q (quality) makes a big difference. I tried with no -Q (default = 0) and -Q 10, and the results were pretty different: Q 10 Geneid Chr Start End Strand Length sorted_mapped_3_rRNA.bam PROKKA_00001 Bin3_16S 1 1 ...
featurecounts rna-seq quality score written 3 months ago by dark.lord30
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Mapping metatranscriptomics rRNA reads to MAG 16S rRNA genes
... Hi all, I have 3 MAGs and I would like to map the metatranscriptomic rRNA reads to the 16S of these 3 MAGs to see whether there is a differential expression - basically a differential expression analyses on 16S instead of functional genes. The procedure I was thinking of involve either kallisto or ...
metatranscriptomics 16s rrna mapping rna-seq written 3 months ago by dark.lord30
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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 24 months ago by dark.lord30
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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 24 months ago by dark.lord30
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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 2.1 years ago by dark.lord30
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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 2.2 years ago by dark.lord30
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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 2.2 years ago by dark.lord30
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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 2.2 years ago by dark.lord30

Latest awards to dark.lord

Popular Question 24 months ago, created a question with more than 1,000 views. For Can I use both paired and single end reads in the same MEGAHIT run?
Popular Question 24 months ago, created a question with more than 1,000 views. For Any tool to assemble 16S rRNA genes at high resolution from metagenomes?
Popular Question 24 months ago, created a question with more than 1,000 views. For Trimmomatic output: how to include unpaired reads in the assembly?

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