Hi - I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, and I can visualize the alignment with E. coli genomes using the UCSC browser. Problem is, I'd like to display the alignment in Artemis, but Artemis doesn't seem to want to read the .BAM file downloaded from Galaxy; I can import my genome sequence but when trying to import the BAM a blank window with "message" in the header keeps popping up. Anyone else tried to do this, and is there something about the Galaxy BAM files that Artemis doesn't like? Thanks. Ed
On Wed, Apr 20, 2011 at 4:00 AM, Edward Dudley <egd100@psu.edu> wrote:
Hi -
I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, and I can visualize the alignment with E. coli genomes using the UCSC browser. Problem is, I'd like to display the alignment in Artemis, but Artemis doesn't seem to want to read the .BAM file downloaded from Galaxy; I can import my genome sequence but when trying to import the BAM a blank window with "message" in the header keeps popping up. Anyone else tried to do this, and is there something about the Galaxy BAM files that Artemis doesn't like?
Thanks.
Ed
Artemis will need the BAM index file (the BAI file). It may also insist on the normal extensions, *.bam and *.bai or *.bam.bai (but not *.dat) Peter
Are you downloading the ³BAI² index file, as well? That might be the problem. Best, Ann On 4/19/11 11:00 PM, "Edward Dudley" <egd100@psu.edu> wrote:
Hi -
I have a set of 454 reads that have been trimmed and converted to BAM format using Galaxy, and I can visualize the alignment with E. coli genomes using the UCSC browser. Problem is, I'd like to display the alignment in Artemis, but Artemis doesn't seem to want to read the .BAM file downloaded from Galaxy; I can import my genome sequence but when trying to import the BAM a blank window with "message" in the header keeps popping up. Anyone else tried to do this, and is there something about the Galaxy BAM files that Artemis doesn't like?
Thanks.
Ed
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participants (3)
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Ann Loraine -
Edward Dudley -
Peter Cock