Hello Theresa,

On the public Main Galaxy instance at https://main.g2.bx.psu.edu/ (usegalaxy.org), ELANDMULTI format is required for paired-end data, and there are no conversion tools available if the alignments are performed with Bowtie.

A good alternative to try is the public Cistrome Galaxy instance at http://cistrome.org/ap/. SAM/BAM input for paired-end data is an accepted in the version of MACS offered there.

I believe the Galaxy Main Tool Shed also has a version of MACS that is similar to the one at Cistrome, for use in a Cloudman Galaxy, but it is down right now so I can't double check for you (is just temporary, will be up soon). But if this interests you, please have a look once up, likely later today.
http://toolshed.g2.bx.psu.edu/

Best,

Jen
Galaxy team

On 6/28/13 7:44 AM, Murphy, Theresa wrote:

Using the Galaxy public server, Is it possible to do peak calling using MACS on Bowtie mapped paired end reads if I do not have access to ELAND to generate ELANDMULTI format. The illumina reads were originally downloaded from the SRA database rather than being generated in house. Is it possible to convert the Bowtie output to ELANDMULTI format?

Thanks,

Theresa Murphy

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org