Question: Bam Files
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gravatar for Edward Dudley
7.2 years ago by
Edward Dudley10 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
galaxy • 1.5k views
ADD COMMENTlink modified 7.2 years ago by Loraine, Ann150 • written 7.2 years ago by Edward Dudley10
0
gravatar for Loraine, Ann
7.2 years ago by
Loraine, Ann150
United States
Loraine, Ann150 wrote:
Are you downloading the łBAI˛ index file, as well? That might be the problem. Best, Ann -- Ann Loraine Associate Professor Dept. of Bioinformatics and Genomics, UNCC North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 www.transvar.org
ADD COMMENTlink written 7.2 years ago by Loraine, Ann150
Hello, First, I've moved this question from the Galaxy development mailing list to the Galaxy user mailing list; in the future, please send questions about using Galaxy to the galaxy-user list. To answer your question, files larger than 2GB must be uploaded via FTP to Galaxy. This is necessary due to Web browser limitations. Help to use FTP is on this wiki. The screencasts both show the two step process. The first is to FTP the data to the server, the second is to move the data from the "Get Data -> Upload Data" tool form into your history. http://wiki.galaxyproject.org/FTPUpload Best, J.
ADD REPLYlink written 4.7 years ago by Jeremy Goecks2.2k
0
gravatar for Peter Cock
7.2 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
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
ADD COMMENTlink written 7.2 years ago by Peter Cock1.4k

if that is indeed the problem, you also can regenerate the BAM index with samtools, like:

samtools index mapped_reads.bam
ADD REPLYlink written 2.9 years ago by wrf0
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