User: predeus
predeus • 860
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Posts by predeus
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... And now there's also AGB: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz072/5306331
...
written 8 days ago by
predeus • 860
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Comment:
C: STAR for bacterial genome
... I think the formula might be over-estimating the value a bit. The number min(14, log2(GenomeLength)/2 - 1) for something like Ecoli/Salmonella should be approximately 10, yet sometimes I get segfaults with this setting. Changing it to 8 fixes everything. ...
written 24 days ago by
predeus • 860
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C: STAR for bacterial genome
... I've made quite a few comparisons, but haven't published them yet.
Briefly, bacterial genomes are quite easy to map to - so uniquely mapped reads don't differ much between bwa/bowtie2/STAR/etc. However STAR/hisat2 are a lot better in reporting multimappers, which could be interesting for highly re ...
written 24 days ago by
predeus • 860
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... Sorry, but I don't understand your arguments.. The main difference for well established genomes and transcriptomes would be speed. And Tophat2 is so, so slow. As far as other things you mentioned,
1) In STAR, you can provide GTF file when generating reference, so when if you really want that known ...
written 7 weeks ago by
predeus • 860
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... Authors of Tophat begged to stop using it. It's a very outdated tool.
https://twitter.com/lpachter/status/937055346987712512?lang=en ...
written 8 weeks ago by
predeus • 860
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... yes, I've ran it with my data and it worked very well (I've ran it against Illumina reads). ...
written 9 weeks ago by
predeus • 860
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... I have just a few contigs - the assembly is almost complete. ...
written 10 weeks ago by
predeus • 860
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... As a matter fact I do have some Illumina! Thank you, very good suggestion. ...
written 10 weeks ago by
predeus • 860
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5 follow
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... Hello all,
I have a Unicycler assembly of a bacterial genome from PacBio and Illumina reads. It's a rather small but repetitive genome, and it's didn't assemble into one circualr chromosome, despite having 500x long read coverage.
I've tried few other options (i.e. long read-only assemblers) and ...
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... Here's something interesting about this solution: **samtools depth has an arbitrary cutoff of 8000!** Anything above that is just discarded. I have no idea why was it made default, and still kind of cannot believe it. If you want your wig file to report true coverage from the BAM file, you would hav ...
written 3 months ago by
predeus • 860
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