Question: MACS giving result for inout data but error in Test data
gravatar for pnkjbsbe
22 months ago by
pnkjbsbe0 wrote:

Hello , I am facing problem when I am trying to use MACS . It is giving data for input data but with test data it showing error

An error occurred with this dataset INFO @ Wed, 18 Jan 2017 12:27:18:


name = MACS_in_Galaxy

format = BAM

ChIP-seq file = /galaxy-repl/main/files/018/508/dataset_18508943.dat

control file = None

effective genome size = 2.70e+09

tag size = 36

band width = 30

Can you help resolving this issue.

chip-seq • 604 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by pnkjbsbe0

Hello, More details about the error are needed to help. Click on the bug icon to see the full error. One option is to post it here for feedback.

Another option, if working at or if you can replicate the problem there, is to send in a bug report. Please include a link to this post in the comments.

Thanks, Jen, Galaxy team

ADD REPLYlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Thanks for sending in the bug report. The error is due to the input content versus the parameters used.

The parameters used with MACS can be test adjusted to better match the input data to ideally produce more called peaks. If the mapped data is sparse (appears to be), lowering the MFOLD is one way to call peaks at a less stringent threshold. The effective genome size in this run was also set to be human. Instead, use the value for rat. See the MACS2 documentation for other ways to tune the parameters.

Best, Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k
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