User: plijnzaad

gravatar for plijnzaad
plijnzaad30
Reputation:
30
Status:
New User
Location:
European Union
Last seen:
2 months, 2 weeks ago
Joined:
1 year, 10 months ago
Email:
p********@gmail.com

Posts by plijnzaad

<prev • 7 results • page 1 of 1 • next >
1
vote
3
answers
449
views
3
answers
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 16 months ago by plijnzaad30
3
votes
3
answers
449
views
3
answers
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 16 months ago by plijnzaad30 • updated 16 months ago by Chris Fields1.8k
0
votes
11
answers
29k
views
11
answers
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 17 months ago by plijnzaad30
0
votes
7
answers
2.3k
views
7
answers
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 17 months ago by plijnzaad30
0
votes
7
answers
2.3k
views
7
answers
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 17 months ago by plijnzaad30
1
vote
3
answers
5.2k
views
3
answers
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 17 months ago by plijnzaad30
1
vote
3
answers
5.2k
views
3
answers
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 17 months ago by plijnzaad30

Latest awards to plijnzaad

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1388 users visited in the last hour