I’m working on a SOLiD ChIP-Seq workflow in which I want to use SICER for peak detection.  In attempting to add SICER to the workflow, I’ve run into some difficulty:


1)       My input is an interval file which I’ve created using Convert SAM.  In order to connect to the SICER module, I had to use a trick by setting up the connection with the Convert SAM set to BED.  The SICER algorithm fails to run when tested with the bed file.  If I then change the connected Convert SAM to interval, SICER will run.

2)      I need to change the default run parameters but they are not saved in the workflow.   There is always reversion to the default values. I get a Server error notice.  This workflow also contains Bowtie and MACS.  Parameter changes for these algorithms are saved correctly.

3)      I would like to run SICER twice in the workflow with different parameters.  Is it allowable to load SICER a second time?  May I run from the same interval conversion file?  I tried this and again could not get the input file recognized as a valid connection.

Thanks in advance,




Susan S. Newman, Laboratory Manager

Genomics Core Facility, L2012

Pennington Biomedical Research Center

6400 Perkins Road

Baton Rouge, LA  70808

225-763-0255 (o) 225-763-0257 (lab)