Hi Peter The sort command runs (slowly) but seperate files are created; Nr32.sorted.0000.bam Nr32.sorted.0001.bam etc
Kind regards, Vriendelijke groeten, John -----Oorspronkelijk bericht----- Van: Peter Cock [mailto:p.j.a.c...@googlemail.com] Verzonden: dinsdag 25 november 2014 10:12 Aan: john@home CC: samtools-help@lists.sourceforge.net Onderwerp: Re: [Samtools-help] sort command On Tue, Nov 25, 2014 at 8:53 AM, john@home <john.groenend...@upcmail.nl> wrote: >> Hi > >> I use the command >samtools index filename.bam and nothing happens >> >samtools sort Nr32.bam >> Usage samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix> >> >> The file is exported from CLC in bam format. The file Nr32.sorted.bam >> is not created. >> >> Do you know what could be wromg? >> Thanks! You probably want to run this command (with no greater than signs): samtools sort Nr32.bam Nr32.sorted That means Nr32.bam is the input BAM file, and Nr32.sorted is the prefix for the sorted output. This will create Nr32.sorted.bam for you. Peter ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
