Hello Carsten, Yes, that is correct. Note that a much better resource for help with samtools and SAM is the samtools-help mailing list: https://lists.sourceforge.net/lists/listinfo/samtools-help
Also, http://samtools.sourceforge.net/ has a link to the specification for SAM/BAM which explains all columns including the numeric flag column. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/23/11 11:42 AM, Carsten Raabe wrote: > dear all, > > I do have question regarding the BAM alignment files specified above. I > converted the BAM file into the SAM file using SAM tools, however I am > not clear which field holds the orientation of the match (read) with > regards to the genome. Would the 16 and 0 in column 2 stand for reverse > and direct orientation respectively?? > > > Thanks a lot in advance, > > Carsten > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
