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
Hi Susan, Sorry for the delay in response. Are you still experiencing these problems? If so, would you mind sharing a history and your workflow with me and I will take a look. Thanks for using Galaxy, Dan On Sep 20, 2011, at 4:28 PM, Susan Newman wrote:
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)
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Daniel Blankenberg -
Susan Newman