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

 

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)

 

http://gcf.pbrc.edu

 

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