User: predeus
predeus • 770
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Posts by predeus
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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 8 days ago by
predeus • 770
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... I have just a few contigs - the assembly is almost complete. ...
written 12 days ago by
predeus • 770
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... As a matter fact I do have some Illumina! Thank you, very good suggestion. ...
written 12 days ago by
predeus • 770
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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 ...
written 4 weeks ago by
predeus • 770
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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 8 weeks ago by
predeus • 770
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... There's a quite widely used tool named [MITObim](https://github.com/chrishah/MITObim).
I know it's an old question, but it keeps popping up in the search, so I figured I'll update it. ...
written 8 weeks ago by
predeus • 770
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... Not any time soon, I'm afraid. Sequencing proteins is the holy grail, but so far it seems very, very hard. ...
written 9 weeks ago by
predeus • 770
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... That's if you doing NGS for biology. If you are doing NGS for medicine, the field would probably be dominated by single-cell RNA-seq. ...
written 9 weeks ago by
predeus • 770
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Comment:
C: Blocking primer design software?
... Unfortunately not. If the primer you require is shorter, then you can get away with mapping - I've mapped 15-mers with bowtie2 onto the groups I was interested in (just 16S from SILVA; you need to use -a option, and it's quite slow, so you would need a reasonable computational power).
But 15nt are ...
written 9 weeks ago by
predeus • 770
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... Guess what, in the newest NAR issue there's a [paper](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1050/5149885) about a plasmid database that is using mash strategy to cluster them. Talk about timing :) ...
written 11 weeks ago by
predeus • 770
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