Do the chromosome names in the BAM and BED files match? Devon -- Devon Ryan, Ph.D. Email: [email protected] Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Mon, Oct 26, 2015 at 8:14 PM, <[email protected]> wrote: > Hello, > > I am trying to get the aligned reads from a bam file for regions specified > in a bed file like this: > > samtools view -h -b -o SJDE001-1-tumor_region1.bam -L region_1.bed > /seq/picard_aggregation/G14865/SJDES001-1/v2/SJDES001-1.bam > > It runs for a long time and it doesn’t produce the output at the end. Is > there a better way to do this? > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
