User: BioinformaticsLad

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Posts by BioinformaticsLad

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Necessary to filter out nanopore (or PacBio) reads before mapping?
... I have some nanopore reads I want to map to hg38 human genome using minimap2. In the past I would filter out mean QV<7 reads but lately I've been thinking: if the reads are long enough, there's little chance that (despite errors) they map to the wrong regions. Is it really necessary to filter the ...
minimap2 alignment mapping nanopore written 17 days ago by BioinformaticsLad130 • updated 12 days ago by Biostar ♦♦ 20
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Comment: C: How do I use Glimmer 3.02?
... Yep, I think to get accurate gene annotations, I'll have to resort to short reads! ...
written 18 days ago by BioinformaticsLad130
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Comment: C: How do I use Glimmer 3.02?
... So I downsampled to 200X, reassembled with Flye and used more specific parameters in Prokka. --kingdom Bacteria --genus Escherichia --usegenus --addgenes --gram neg I still get ~10000 CDS in my Prokka output. I guess we can rule out coverage messing up the assembly. ...
written 19 days ago by BioinformaticsLad130
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Comment: C: How do I use Glimmer 3.02?
... That's right, although I'm mainly interested in using E. coli as pipeline validation. If I can get decent results with E. coli then I could be more confident going forwards that novel genomes, for which I don't have a reference, would do similarly well. ...
written 19 days ago by BioinformaticsLad130
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Comment: C: Programs for bacterial gene prediction/annotation for nanopore assembly?
... Flye, the new kid on the block. Benchmarks say it's the 'best' for nanopore bacterial genomes. I tried Canu as well and it was okay but didn't match up to the reference as well as Flye (and also took way longer). Sure, let me try downsampling and reassemble, see if that's the problem. ...
written 19 days ago by BioinformaticsLad130
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Comment: C: Programs for bacterial gene prediction/annotation for nanopore assembly?
... That's a good suggestion. ...
written 19 days ago by BioinformaticsLad130
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Comment: C: How do I use Glimmer 3.02?
... Good point, although I'm not sure that would help. From a macro level, the assembly is correct. Substitution errors are also fairly low, considering these are nanopore reads. The problem is still the indels errors which are systemic to nanopore reads causing frameshifts. I'm just surprised that they ...
written 19 days ago by BioinformaticsLad130
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Comment: C: Programs for bacterial gene prediction/annotation for nanopore assembly?
... Thanks, nanopore-only assemblies are indeed problematic. However, what confuses me is if we consider that 90% of most bacterial genomes are actual genes (5000), how can Prokka finds the same number of genes (5000 pseudogenes) in the remaining 10% of the genome? Unless it accounts for overlapping rea ...
written 19 days ago by BioinformaticsLad130
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Comment: C: How do I use Glimmer 3.02?
... Coverage is more than a 1000X, which is quite excessive. It ended up almost exactly as long as the reference, ~5Mb. Thanks! Let me try play around with the parameters. ...
written 19 days ago by BioinformaticsLad130
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Comment: C: How do I use Glimmer 3.02?
... It's a single contig! I also thought Prokka would be more conservative. Maybe it's the parameters I'm *not* using? I'm using the most basic command: % prokka contigs.fa ...
written 19 days ago by BioinformaticsLad130

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Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Guppy basecaller ONT
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