Hi Nripesh, The reference file is the source genome or any other fasta file that your data is derived from (could be custom). It is the "reference" sequence that you will be using for mapping. There are a few thing to try: If your data will be mapped to a genome already in Galaxy, then use the pencil icon (for the SAM history item) and alter the attributes to assign a genome. Next, use the same genome as the reference when running SAM->BAM. Please note that not all genomes are indexed for use by SAM tools. If your genome is not here, we are open to requests to add more, if the data is in our main genome list or publicly available from a stable source. Please be specific for requests - exact genome name as we use it, or a link to NCBI, or a link to another public data source is preferred. If your data is custom, the database can remain undefined (will display as a "?"). Load your custom fasta genome/sequence into your history, if not already there. Then when running SAM->BAM, use the option "locally cashed" and set the reference to be that loaded custom fasta file. Hopefully this helps to resolve the issue. But, if you continue to have problems, please feel free to share your history and we can take a closer look. To do this, at the top of the history pane (right): Options -> Share or Publish -> Make History Accessible via Link and email to me. Thanks! Jen Galaxy team On 11/8/10 12:20 PM, Nripesh Prasad wrote:

Hii Jennifer, I am doing it that way only, i have uploaded my .sam files in history, now when i select NGS: SAM Tools -> SAM-to-BAM, it gives me two options to choose the source, if i select history and enter the sam file then it is asking for a reference file, What is a reference file adn where do i get a reference file ? if i do it by the option locally cached as a source then it is giving me following error.

*Error(s):*

* No Content-Length: returned in header for http://main.g2.bx.psu.edu/display_application/41246453625d8c97/ucsc_bam/main..., can't proceed, sorry

what shopuld i do now? Nripesh On Mon, Nov 8, 2010 at 2:14 PM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:

Hi Nripesh,

Use "NGS: SAM Tools -> SAM-to-BAM". This will create a new BAM data history item.

Hope this helps!

Jen Galaxy team

ps. For new data/usage questions, it would be great for us if you could send them to the mailing list galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu>. We like to publish answers there for other all to learn from.

On 11/8/10 11:31 AM, Nripesh Prasad wrote:

Hii Jennifer, How can i convert .sam format to .bam format in galaxy. Nripesh

-- Jennifer Jackson http://usegalaxy.org <http://usegalaxy.org/>

-- Jennifer Jackson http://usegalaxy.org