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.kna...@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,
> 
> Kamila
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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


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

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