User: predeus

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predeus770
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Russia
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http://bioinf.me/research
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APredeus
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14 hours ago
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6 years, 2 months ago
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Posts by predeus

<prev • 106 results • page 1 of 11 • next >
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Comment: C: Using Bandage to finish ambiguous long-read assembly?
... 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 predeus770
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Comment: C: Using Bandage to finish ambiguous long-read assembly?
... I have just a few contigs - the assembly is almost complete. ...
written 12 days ago by predeus770
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Comment: C: Using Bandage to finish ambiguous long-read assembly?
... As a matter fact I do have some Illumina! Thank you, very good suggestion. ...
written 12 days ago by predeus770
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Using Bandage to finish ambiguous long-read assembly?
... 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 ...
unicycler assembly long reads bandage written 4 weeks ago by predeus770
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Comment: C: How Can I Convert Bam/Sam To Wiggle
... 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 predeus770
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Answer: A: What Is The Best Way To Detect Mitochondrial/Chloroplast Genomes From Assembled
... 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 predeus770
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Comment: C: Where and how NGS techniques are heading for the next 5 years?
... 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 predeus770
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Comment: C: What would be the trend in next few years in NGS era?
... 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 predeus770
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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 predeus770
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Comment: C: Cluster plasmids of (very) different lengths
... 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 predeus770

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Get a complete GSM-to-SRX/SRR table
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