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)





Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to