Hi David & Colin, Thank you for your generous help. It works.
Daniel Chau On 6 April 2016 at 16:36, David Jones <[email protected]> wrote: > Hi Daniel, > > Looking at the reads in the attached sam file you have only 4 reads marked > as ‘properly paired’. You can establish this by looking at the values in > the FLAG field for each read. > By default mpileup excludes these ‘anomalous’ (not properly paired) reads. > > If you to add -A to your command you would see all of the reads are > included in the pileup (see attached). > > samtools mpileup -Q0 -A t.sam > t2.pileup > > David Jones > [email protected] > > Principal Bioinformatician > Cancer Genome Project (Team 78) > Wellcome Trust Sanger Institute > Wellcome Trust Genome Campus > Hinxton > Cambridge > CB10 1SA > UK > > > -- 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. > > > On 6 Apr 2016, at 06:28, Daniel Chau <[email protected]> wrote: > > Hello everyone, > > I am an undergrad and newbie to bioinformatics. Recently I encountered a > problem that I could not solve on myself. > > A pileup file was generated by this command: > > samtools mpileup -Q0 -f ucsc.hg19.fasta t.sam > t.pileup > > . There are 9 alignment items in that sam file, but only 4 of them are > shown in the pileup file. > > Both the sam file and the pileup file are attached. Sum of them are > smaller than 1MB. > > I really hope you could help me and tell me why whose 5 alignment items > are abandoned by samtools. > > Sincere appreciation. > > Daniel Chau > > <t.pileup><t.sam> > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > >
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