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
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