Thank you! My mistake.. I didnt see that.. On Tue, Oct 28, 2014 at 1:17 PM, Devon Ryan <dpr...@dpryan.com> wrote:
> Hi Dror, > > You're misunderstanding what the portion before the decimal does. It's the > seed to the RNG, it doesn't specify the portion to subsample. The portion > after the decimal says what portion to subsample (after all, a subsample > can't be more than the input sample...by definition). So -s 1.5, -s 0.5, > and -s 100.5 will all subsample ~50% of the original file, but with > different starting seeds (1, 0, and 100, respectively). > > file1/file2 will only differ if they have a different starting seed. If > you tried: > > samtools view -s 0.5 foo > foo1 > samtools view -s 1.5 foo > foo2 > > then you'd find that they have similar numbers of alignments (as expected, > you're subsampling ~50% of the reads in each case) but that they're not > identical (due to seeding the RNG with 0 and 1, respectively). > > BTW, 0.1.19 is two versions behind the current release. > > Devon > > -- > Devon Ryan, Ph.D. > Email: dpr...@dpryan.com > Laboratory for Molecular and Cellular Cognition > German Centre for Neurodegenerative Diseases (DZNE) > Ludwig-Erhard-Allee 2 > 53175 Bonn > Germany > <devon.r...@dzne.de> > > On Tue, Oct 28, 2014 at 12:05 PM, Dror Hibsh <dro...@gmail.com> wrote: > >> Hi guys, >> >> My samtools version is: 0.1.19-44428cd >> >> I am trying to use the '-s' option.. >> >> My bam file has: >> samtools view Example.bam | wc -l >> 2000000 >> >> samtools view -s 0.5 Example.bam | wc -l >> 1001528 >> samtools view -s 1.5 Example.bam | wc -l >> 998410 >> samtools view -s 2.5 Example.bam | wc -l >> 998744 >> >> I cant understand the results.. >> -s 0.5 should produce exactly 1000000 reads >> and 1.5 should be 3000000 etc.. >> >> Am i missing somthing? >> Moreover, >> samtools view -s 0.5 Example.bam > file1 >> samtools view -s 0.5 Example.bam > file2 >> file1 file2 are identical.. Isnt -s should be random subsampling??? >> >> Actually i saw this issue in some threads as solved, but it doesnt solve >> for me.. >> https://github.com/samtools/samtools/issues/160 (for example) >> >> >> Thanks, >> Pap >> >> >> >> >> >> >> >> -- >> ----------------- >> Dror Hibsh >> 0507-669599 >> ------------------ >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Samtools-help mailing list >> Samtools-help@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/samtools-help >> >> > -- ----------------- Dror Hibsh 0507-669599 ------------------
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