Hi AP,

SICER requires BED formatted input with at least 6 columns (for strand 
information). You can convert your BAM files into SAM and then into interval 
and BED format. Once you have your input in the BED (6+) format, you should be 
able to use these tools.  Please let us know if we can provide additional 
information.


Thanks for using Galaxy,

Dan



On Nov 23, 2011, at 12:26 PM, Anupam Paliwal wrote:

> Hi,
> 
> I want to use SICER or Find Peaks for peak calling on GALAXY.
> 
> I am using my aligned ChIP-seq tag .BAM files. However for both the tools
> the history is unable to pick the Bowtie-ligned SAM to BAM converted
> files.
> 
> On the other hand, using MACS the same files are working nicely for peak
> calling.
> 
> Thanks,
> 
> AP
> 
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