Thanks Colin, I think you are right.
Xinan Liu On Mon, May 26, 2014 at 11:11 PM, Colin Hercus <co...@novocraft.com> wrote: > Hi Xinan, > > I'd also like to have a clearer definition of at least NH. > > In Novoalign we have interpreted NH as the number of alignments to the query > sequence that are equivalent to the best alignment. These may not all be > reported in the SAM file. > > So if we find 100 alignments but create SAM records for only 10 then NH is > 100 and IH is 10. > > I've never checked what other aligners do with NH. > > Kind Regards, Colin > > > > On 21 May 2014 21:47, Xinan Liu <hitcs...@gmail.com> wrote: >> >> Hello, >> >> I am a little confused about the difference between NH and IH tags in >> SAM format. >> >> NH: Number of reported alignments that contains the query in the current >> record >> IH: Number of stored alignments in SAM that contains the query in the >> current record >> >> Some aligners are using NH, and some other aligners are using IH. So >> what's the difference between them? Thanks. >> >> -- >> Xinan Liu >> >> >> ------------------------------------------------------------------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. >> Get unparalleled scalability from the best Selenium testing platform >> available >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> _______________________________________________ >> Samtools-help mailing list >> Samtools-help@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/samtools-help > > -- Xinan Liu ------------------------------------------------------------------------------ The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
