Hi, If you download the BAM file and it's index ("BAI") file onto your desktop, you should be able to open it directly in Integrated Genome Browser. Just be sure to put the BAM and its BAI file in the same folder. If you run into any problems, please let us know. You can post a message on the IGB forum or email me directly if you like. IGB Forum is: http://sourceforge.net/projects/genoviz/forums/forum/439786 A question: Do you want to align your reads onto a several different bacterial genomes, in addition to B3? Best wishes, Ann Loraine On 4/10/11 10:56 AM, "Kamila Knapik" <kamila.knapik@gmail.com> wrote:

Hello,

I am trying to map metagenomic Illumina reads to the reference genomes. I used Galaxy LASTZ tool to align Illumina reads to bacteriophage B3, that genomic sequence I downloaded from NCBI website. LASTZ produced an output file in SAM format, the file size is 1.8 MB and contain 16,000 lines. Then, I used Galaxy SAM tools to converted SAM to BAM, and now I am trying to visualize the BAM file in e.g. BamView or Integrated Genome Browser, but without any success. Can anybody tell me what I am doing wrong or how to visualize the alignment, please?

Thank you,

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-- 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