After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this? Thanks, Andrew
Hi Andrew, Is this on a local instance or the public Main Galaxy instance at usegalaxy.org (https://main.g2.bx.psu.edu)? Also, the exact tools being used and the order is not clear. Maybe a step is missing from what is listed? (I am just guessing) If you are using the public Main instance, you can share a history with me and I can provide feedback. If this is on your instance, could you list the tools by name, in the order used, with key parameters (e.g. "Generate pileup from BAM dataset" with option 10-column pileup)? It sounds like there might be a mix-up about the file formats being used as inputs to tools. It may be something that can be resolved by reassigning the datatype or by adjusting the tool(s) used. Best, Jen Galaxy team On 6/24/13 1:10 PM, Andrew Guo wrote:
After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this?
Thanks, Andrew
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-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
This is on the public instance. I can share my history with you right here... https://main.g2.bx.psu.edu/u/guotaek/h/galaxy-101 On Mon, Jun 24, 2013 at 6:40 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Andrew,
Is this on a local instance or the public Main Galaxy instance at usegalaxy.org (https://main.g2.bx.psu.edu)?
Also, the exact tools being used and the order is not clear. Maybe a step is missing from what is listed? (I am just guessing) If you are using the public Main instance, you can share a history with me and I can provide feedback. If this is on your instance, could you list the tools by name, in the order used, with key parameters (e.g. "Generate pileup from BAM dataset" with option 10-column pileup)?
It sounds like there might be a mix-up about the file formats being used as inputs to tools. It may be something that can be resolved by reassigning the datatype or by adjusting the tool(s) used.
Best,
Jen Galaxy team
On 6/24/13 1:10 PM, Andrew Guo wrote:
After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this?
Thanks, Andrew
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson Galaxy Support and Traininghttp://galaxyproject.org
Hi Andrew, If you want to run the tool "Filter pileup on coverage and SNPs" on dataset #21, change the datatype to be "pileup". Then it will show up under the list of inputs. Be sure to set the forms options for a 10-column pileup input when you run it. Change the datatype by clicking on the pencil icon for the dataset, to open the Edit Attributes form in the center panel. Click on the "Datatype" tab, then enter pileup, select it from the list, and save. Allow the metadata to finish detecting on it's own. Hopefully this helps, Jen Galaxy team On 6/24/13 5:11 PM, Andrew Guo wrote:
This is on the public instance. I can share my history with you right here...
https://main.g2.bx.psu.edu/u/guotaek/h/galaxy-101
On Mon, Jun 24, 2013 at 6:40 PM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Hi Andrew,
Is this on a local instance or the public Main Galaxy instance at usegalaxy.org <http://usegalaxy.org> (https://main.g2.bx.psu.edu)?
Also, the exact tools being used and the order is not clear. Maybe a step is missing from what is listed? (I am just guessing) If you are using the public Main instance, you can share a history with me and I can provide feedback. If this is on your instance, could you list the tools by name, in the order used, with key parameters (e.g. "Generate pileup from BAM dataset" with option 10-column pileup)?
It sounds like there might be a mix-up about the file formats being used as inputs to tools. It may be something that can be resolved by reassigning the datatype or by adjusting the tool(s) used.
Best,
Jen Galaxy team
On 6/24/13 1:10 PM, Andrew Guo wrote:
After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this?
Thanks, Andrew
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
Thanks for the help! Worked fine after that. On Mon, Jun 24, 2013 at 7:23 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Andrew,
If you want to run the tool "Filter pileup on coverage and SNPs" on dataset #21, change the datatype to be "pileup". Then it will show up under the list of inputs. Be sure to set the forms options for a 10-column pileup input when you run it.
Change the datatype by clicking on the pencil icon for the dataset, to open the Edit Attributes form in the center panel. Click on the "Datatype" tab, then enter pileup, select it from the list, and save. Allow the metadata to finish detecting on it's own.
Hopefully this helps,
Jen Galaxy team
On 6/24/13 5:11 PM, Andrew Guo wrote:
This is on the public instance. I can share my history with you right here...
https://main.g2.bx.psu.edu/u/guotaek/h/galaxy-101
On Mon, Jun 24, 2013 at 6:40 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Andrew,
Is this on a local instance or the public Main Galaxy instance at usegalaxy.org (https://main.g2.bx.psu.edu)?
Also, the exact tools being used and the order is not clear. Maybe a step is missing from what is listed? (I am just guessing) If you are using the public Main instance, you can share a history with me and I can provide feedback. If this is on your instance, could you list the tools by name, in the order used, with key parameters (e.g. "Generate pileup from BAM dataset" with option 10-column pileup)?
It sounds like there might be a mix-up about the file formats being used as inputs to tools. It may be something that can be resolved by reassigning the datatype or by adjusting the tool(s) used.
Best,
Jen Galaxy team
On 6/24/13 1:10 PM, Andrew Guo wrote:
After using tools to convert a SAM to a BAM file, I am trying to filter the BAM pileup. However, the filter BAM tool is not picking up on the dataset that I just created. It should show up under 10 column pileup, but an error message is saying "History does not include a dataset of the required format/build". Could you provide any insight into this?
Thanks, Andrew
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson Galaxy Support and Traininghttp://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Traininghttp://galaxyproject.org
participants (2)
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Jennifer Jackson