User: predeus

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predeus590
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Posts by predeus

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Best way to assign pfam/EC/COGs to a set of proteins
... This is basically a bacterial pan-genome - all the predicted proteins, with 100% redundant proteins removed, but not more - I'm experimenting with species-specific paralog discrimination. It's quite massive and would have lots and lots of hits with nr, I am sure. ...
written 6 days ago by predeus590
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Comment: C: Best way to assign pfam/EC/COGs to a set of proteins
... Thank you, good tip! I don't have much experience with nr, but wouldn't it just give me a list of matches to nr proteins? Or are all nr proteins assigned EC or COG? I've seen COG/OrthoMCL and few other old protein clustering software packages, but I was curious if there is a streamlined way to d ...
written 6 days ago by predeus590
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Answer: A: Need help in GSEA analysis and interpretation
... What do you mean by "significant genes"? Are they significant in differential expression analysis? Because GSEA does not generate significant genes, GSEA gives you **leading edge** genes, and that's different. Overall, you need to specify 1) what GSEA tool and method have you used; 2) what was th ...
written 6 days ago by predeus590
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Best way to assign pfam/EC/COGs to a set of proteins
... Hello all, I am working on a large-scale project that involves annotation of a large array of proteins, many of them of unknown function. I was wondering if there's a good way to assign pfam groups, GOGs, and enzyme commission (EC) number to the proteins where possible, so I won't have to rely on ...
pfam protein enzyme cog written 7 days ago by predeus590 • updated 6 days ago by genomax52k
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Answer: A: Which software to use to map 100bp DNA sequence to genome
... Every time I see someone using Tophat or suggesting using it (unless you're dealing with colorspace RNA-seq) I cringe a little :) Bwa does better job estimating mapping quality, which is pretty important for variant calling. Otherwise, any genomic aligner that's well supported would do equally well. ...
written 7 weeks ago by predeus590
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Answer: A: STAR for chip-seq
... "too short" is STAR's euphemism for reads that just fail to align. What's the alignment rate you're getting with bowtie2? Chip-Seq is very tricky experimentally, so it happens quite often that libraries are full of adapter sequences etc. Aligners (as long as you are using a well-supported modern one ...
written 7 weeks ago by predeus590
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Comment: C: Racon-Illumina or Pilon?
... Very useful insight and link, thank you! The fact about many rounds of Pilon polishing is particularly interesting, since Unicycler (that performs exceptionally for hybrid bacterial assembly) does use this exact strategy (polishing with Pilon until convergence, i.e. there are no more changes happe ...
written 7 weeks ago by predeus590
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Racon-Illumina or Pilon?
... Hello all, I was experimenting with various options to improve Nanopore-based assembly by short reads (Illumina). It appears like there are options now to use Racon with Illumina, or to use Pilon. Does anybody know which one is better? Any other suggestions from experience? Thank you in adva ...
assembly polishing nanopore written 7 weeks ago by predeus590
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Huge jump in plasmid coverage - any idea why?
... Hello all, I am working on some bacterial genome assemblies that have been assembled using Pacbio reads only. I realized that I can make minor improvements to them (on the order of several SNPs and indels) by aligning Illumina data from the same strain to Pacbio assembly, and polishing it with Pil ...
pilon illumina bacteria pacbio written 4 months ago by predeus590
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Comment: C: Modern software for whole genome alignment visualization
... SNPs and indels with annotations (silent/missense/nonsense, frameshift/in-frame), for example. ...
written 4 months ago by predeus590

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