Hello, Kirthi. While we do not have a tool that converts from BAM to BED, if you were looking to extract coordinates from a BAM file, you could try using SAMtools (http://samtools.sourceforge.net/). Please direct any SAMtools-related questions toward the people who maintain that tool. Once you have extracted the coordinates from your BAM file(s), you can put them in BED format. The FAQ at http://genome.ucsc.edu/FAQ/FAQformat.html#format1 describes and provides an example of a file in BED format. You may also be interested in our BAM format page here: http://genome.ucsc.edu/goldenPath/help/bam.html.
Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pulakanti, Kirthi Sent: Wednesday, January 04, 2012 7:28 AM To: [email protected] Subject: [Genome] .bam file to .bed file Hello: I have just downloaded the .bam file from mm9 database that is the UW DNAse I Hypersensitivity for Embroyonic stem cells in mouse. SO my question is how can I convert the .bam file to .bed file. Can I use BED tools for this . The reason I am asking you this is the files from ENCODE are different with their indexes and all. SO is it ok to convert .bam to .bed file using any conversion tool(BED tools) Thanks for your time Kirthi -- *********** CONFIDENTIALITY NOTICE *********** This transmission may contain confidential information. If you have received this transmission in error, please notify the sender immediately and destroy this material. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
