Moderator: 5heikki
5heikki ♦ 7.8k
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Posts by 5heikki
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... Perhaps you're supposed to compare the ORF annotations, percent that intersect, percent unique to either method, etc. ...
written 26 days ago by
5heikki ♦ 7.8k
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Comment:
C: standalone blast output to excel
... Yes, just use `-outfmt 6` or `-outfmt 10` for tab or comma separated values and import to excel accordingly. You also need to define the output fields you're interested in. You can see all options with `blastn -help` ...
written 29 days ago by
5heikki ♦ 7.8k
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... You mean like Silva's [Living Tree][1]?
[1]: https://www.arb-silva.de/projects/living-tree/ ...
written 4 weeks ago by
5heikki ♦ 7.8k
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... Yeah, but the option is basically useless as it is. Like, in what kind of use case would the output make sense? Why not have an option `-max_random_hits` while at it.. ...
written 5 weeks ago by
5heikki ♦ 7.8k
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... My bad for not noticing the previous posts. Anyway, I think this issue deserves a lot of visibility. Like one of those previous posts could be a sticky until NCBI does something about it.. ...
written 5 weeks ago by
5heikki ♦ 7.8k
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... > To our surprise, we have recently discovered that this intuition is incorrect. Instead, BLAST returns the first N hits that exceed the specified E-value threshold, which may or may not be the highest scoring N hits. The invocation using the parameter "-max_target_seqs 1" simply returns the firs ...
written 5 weeks ago by
5heikki ♦ 7.8k
• updated
5 weeks ago by
Devon Ryan ♦ 86k
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... What's enough RAM though? This week I noticed that 256GB isn't enough RAM for e.g. indexing a large reference with default Bowtie2 settings. Sure I can increase offrate but it goes directly against my aims.. ...
written 5 weeks ago by
5heikki ♦ 7.8k
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... Did you create it with the `parse_seqids` flag? I recall it taking way longer than a few hours. The compression part shouldn't take that long since it can be parallelized ...
written 5 weeks ago by
5heikki ♦ 7.8k
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Comment:
C: primers for whole metagenome
... It's a step you perform prior to any sequencing ...
written 5 weeks ago by
5heikki ♦ 7.8k
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Comment:
C: primers for whole metagenome
... This is not a bioinformatics question. Anyway, buy some multiple displacement amplification kit ([just be aware of its shortcomings][1])..
[1]: https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-3 ...
written 6 weeks ago by
5heikki ♦ 7.8k
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