User: plijnzaad

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plijnzaad30
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Location:
European Union
Last seen:
4 months, 3 weeks ago
Joined:
2 years ago
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p********@gmail.com

Posts by plijnzaad

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Is the EMBOSS project still alive?
... Yes, this appears to be the case, thanks. BTW, I also got e-mail bounces from : 421 4.4.0 [internal] no MXs for this domain could be reached at this time (and also postmaster and webmaster). I'll ask/notify the EBI people. Cheers, Philip ...
written 18 months ago by plijnzaad30
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Is the EMBOSS project still alive?
... Dear all, is the EMBOSS project still alive? I can't download the latest tarball (broken link), the mailing list manager is broken (so I cannot subscribe to ask the question), and their CVS server gives a time-out. Does anyone know? Cheers, Philip ...
software error written 18 months ago by plijnzaad30 • updated 18 months ago by Chris Fields1.8k
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Answer: A: Selecting Random Pairs From Fastq?
... Dunno if still relevant, but I remember having written a tool for this that used one pass rejection sampling, see https://github.com/plijnzaad/phtools/blob/master/ngs/fastq-subsample-paired.pl ...
written 19 months ago by plijnzaad30
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Answer: A: randomly shuffle BAM file
... Oh, and I just see that `samtools view` has an option -s SEED.percentage -s FLOAT integer part sets seed of random number generator [0]; rest sets fraction of templates to subsample [no subsampling] This is prolly the fastest way to do it. ...
written 19 months ago by plijnzaad30
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Answer: A: randomly shuffle BAM file
... I tend to specify a fraction of whatever lines I want (which I have to know in advance), and then use rejection sampling (i.e., if (rand() > fraction) { print it }; ).This can use stdin and stdout, is exceedlingly fast, but maintains the original order. If that is undesirable, you can as yet sub ...
written 19 months ago by plijnzaad30
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Comment: C: Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
... Hi, I got confused a bit myself regarding the difference between picard sort order and Unix sort order. It turns out to be slightly nasty. Picard sort uses ASCII sort order, whereas the Unix sort uses 'lexicographic' order, which depends on the locale. The nasty bit is that in many locales, includi ...
written 19 months ago by plijnzaad30
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Comment: C: Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
... > samtools -n: Uses an ASCII sort. No, this is certainly not true, see e.g. https://github.com/samtools/hts-specs/issues/5 Samtools does a natural sort per subfield (which are separated by ':'), i.e. lexicographic sort for string-subfields, and numeric sort for integer sub-field. (Very annoying ...
written 19 months ago by plijnzaad30

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