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Question: Unable To Run Sicer Or Find Peaks
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gravatar for Anupam Paliwal
7.0 years ago by
Anupam Paliwal • 10
Anupam Paliwal • 10 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
alignment bowtie • 2.6k views
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modified 4.6 years ago by Galaxy Community ♦♦ 0 • written 7.0 years ago by Anupam Paliwal • 10
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gravatar for Daniel Blankenberg
7.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
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
ADD COMMENT • link written 7.0 years ago by Daniel Blankenberg ♦♦ 1.7k
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gravatar for Daniel Blankenberg
7.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
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, Dan
ADD COMMENT • link written 7.0 years ago by Daniel Blankenberg ♦♦ 1.7k
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