Hi AP,

Please keep all replies on list, this will allow the community to assist and benefit from these correspondences. 

SICER requires BED input. To go from BAM to BED:
1.) Convert BAM to SAM
2.) Convert SAM to Interval (Convert SAM to interval)
3.) Convert interval to BED(6+). This can be done by implicitly (by selecting the Interval dataset, which will be marked with '(as bed)' in the SICER input box) or by clicking on the pencil icon and explicitly converting uder the section "Convert to new format".

Please let us know if we can provide additional assistance.

Thanks for using Galaxy,


On Nov 29, 2011, at 1:23 PM, Anupam Paliwal wrote:

Hi Daniel,

Thanks for your kind attention and advice.

I have followed the following workflow:  I aligned my query sequences to
the reference genome using Bowtie; the Bowtie aligned SAM file was
subjected to filter-SAM before converting it to BAM. I have re-BAM-to-SAM
converted the BAM-file before subjecting it to pileup.

However, now I do have the Input format file (after pileup of SAM) but am
unable to convert it to BAM format to be able to submit it ti SICER.

Please see if you can suggest how to convert the Input files back to BAM.
I have tried changing directly through edit-attributes, but it shows


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,


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


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
the history is unable to pick the Bowtie-ligned SAM to BAM converted

On the other hand, using MACS the same files are working nicely for peak



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:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at: