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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