That probably means all the data in your in.bam is flagged READ1 or READ2, so you need to specify the -1 and -2 options.
> On 1 Feb 2016, at 10:00, Robert May <[email protected]> wrote: > > > fastq/a > samtools fastq [options] in.bam > samtools fasta [options] in.bam > Converts a BAM or CRAM into either FASTQ or FASTA format depending on the > command invoked. > > using this command (0=zero fasta=.fa or.fai) > > samtools fasta -n -0 out .fai in.fasta > > the result I get if that the .fa or .fai file is created with o KB but the > fasta is printed to the screen. > > I cant see any other options > any ideas > > Bob May > DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler > Surname and ISOGG YTree > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
