User: predeus

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predeus690
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http://bioinf.me/research
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Posts by predeus

<prev • 102 results • page 2 of 11 • next >
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Answer: A: Bacterial GWAS analysis?
... Here's a nice review that mentions many important papers in bacterial GWAS, and does a pretty good job explaining the difference between human GWAS and various attempts to do this in bacteria. https://figshare.com/articles/The_background_of_bacterial_GWAS/5550037 ...
written 11 weeks ago by predeus690
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Comment: C: Modern software for whole genome alignment visualization
... Nothing outside what was mentioned here, no. This tool was useful: https://dnanexus.github.io/dot/ it uses Nucmer alignments and creates a pretty useful visualization. ...
written 3 months ago by predeus690
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Comment: C: Options for long-read diploid assembly
... Not just long reads - there's plenty of assemblers for that (and, no offence, but I would not rank the options you mentioned too highly - miniasm-racon is way faster, and Flye and Canu a a lot more user friendly and generate better results). However, I was interested in tools specifically geared tow ...
written 3 months ago by predeus690
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Options for long-read diploid assembly
... Hello all, I was wondering about the options for ploidy-aware assemblers for long reads. I know there is FALCON-unzip for Pacbio, and I also have seen a [recent preprint][1]. What are other options for highly heterozygous genomes? Thank you in advance! [1]: https://www.biorxiv.org/content/earl ...
assembly diploid pacbio nanopore written 3 months ago by predeus690 • updated 3 months ago by harish130
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Answer: A: Reporting of multiple alignments using hisat2
... This is actually one of the most confusing things about alignment in general. What this description means (I think) is that if you have -k set to 10, and aligner will find 10 locations where the read aligns with a certain mapping score, it will report them and stop looking further. What I do not ...
written 4 months ago by predeus690
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Comment: C: Using Hisat2 with strand specific bacteria sequences
... There's an interesting caveat I just discovered. Apparently, bwa and bowtie2 do not add NH tag to the resulting SAM/BAM files (that's the flag indicating how many times did this particular read ID was reported mapped - so, simply put, it's important to keep track of the multimapping reads). So, an ...
written 4 months ago by predeus690
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Answer: A: Gene official symbols and uncharacterised genes in the Salmonella annotations
... Unfortunately, it is never safe to assume such things with bacterial gene names. In your own list, SL0471 is identified as aefA - this should be its name, unless there's one that is used more often. SL identifiers are from SL1344 strain. You can take another 10-20 reference strains from NCBI and ...
written 4 months ago by predeus690
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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 4 months ago by predeus690
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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 4 months ago by predeus690
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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 4 months ago by predeus690

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