Moderator: 5heikki

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5heikki7.6k
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Posts by 5heikki

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Comment: C: How to perform metagenomic binning using ESOM?
... The U-matrix or whatever presentations of the ESOMs themselves don't really serve any purpose apart from looking cool. You're correct about MaxBin not producing ESOMs. However, the ultimate goal, i.e. binning, is the same. I don't remember exactly what I did as it was many years ago. That script at ...
written 5 days ago by 5heikki7.6k
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Answer: A: How to perform metagenomic binning using ESOM?
... 1. No 2. No, it says "if you plan to use it" 3. That paper you posted yourself and the related [git][1] A few years ago I did some ESOM stuff based on that very paper. In the end I realized that other programs such as [MaxBin][2] were far easier/more convenient to use and gave better results (at le ...
written 5 days ago by 5heikki7.6k
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Comment: C: I Wonder Why It Is So Important To Use Seq Objects In Stead Of Plain Ol' Strings
... Great answer. OOP always felt stupid to me, like why increase the complexity of the program.. I suppose there comes a point where OOP actually decreases complexity, but the commonly referred to a few hundred LOC isn't it, IMO. Maybe around 1k LOC you cross the point where OOP actually helps.. ...
written 12 days ago by 5heikki7.6k
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Comment: C: Removing everything after the last underscore in the header of a fastafile
... Sure, `BEGIN{OFS=FS="_"}` Before anything is read, underscore is set as field separator (`FS`) and output field separator (`OFS`). If `OFS` was omitted it would default to space and we would have `>ART01B 100 M7 ID100005` instead of `>ART01B_100_M7_ID100005` `{if(/^>/){NF--}}` If a line b ...
written 13 days ago by 5heikki7.6k
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Answer: A: Removing everything after the last underscore in the header of a fastafile
... awk 'BEGIN{OFS=FS="_"}{if(/^>/){NF--}}{print $0}' in.fa > out.fa ...
written 13 days ago by 5heikki7.6k
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Comment: C: What server do you use?
... Is it possible to change a job after it has been submitted to a PBS queue? If yes, you could set up e.g. crontab to submit a `echo "hello"` job every few hours. Then whenever you need to run something you could modify the submitted job that is next up. A nice (pun sort of) admin wouldn't bother you ...
written 15 days ago by 5heikki7.6k
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Comment: C: What server do you use?
... I really hate it when people do that. Just because it's free right now, doesn't mean that it's free five minutes from now. SGE wouldn't see your work thou so our jobs would end up competing for resources. It's ok for very small stuff. Everything else, absolute NO! ...
written 15 days ago by 5heikki7.6k
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Answer: A: Find 12-mer not mapping to the human genome
... 1. Fragment the human genome into 12-mers with e.g. [jellyfish][1] 2. Generate all possible 12-mers with e.g. [this][2] 3. Use `comm` to get lines unique to your all 12-mers file I don't know what you mean by "not forming self-mer".. [1]: https://github.com/gmarcais/Jellyfish [2]: https://stac ...
written 20 days ago by 5heikki7.6k
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Comment: C: Pseudogenes in bacteria genome
... IMO any ORF that is never transcribed to mRNA can be described as a pseudogene. It doesn't have to exist as multiple copies or anything.. ...
written 22 days ago by 5heikki7.6k
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Comment: C: How to use GNU parallel to download SRA files
... IMO in general there's no point to try to parallelize downloads. It will not magically increase your download bandwidth, nor increase the speed at which any decently configured server serves you files. Instead, it might lead to the server flagging you and banning your IP address ...
written 23 days ago by 5heikki7.6k

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