Hi Jacqui,
The "NGS: SAM Tools -> Filter pileup" tool was corrected last September
to require input datasets to be assigned to the format "pileup". Is
there a chance that these datasets are not? Maybe imported or
manipulated by other tools, resulting in another datatype assignment
(tabular or other)? The datatype is noted directly under the dataset
name, in each dataset's box in the history.
If so, you can reassign the format (as long as it meets specification,
see the tool "NGS: SAM Tools -> Generate pileup" for a description), by
clicking on the pencil icon for a dataset, then the tab "Datatype", and
assigning "pileup" manually (don't forget to save). This will help with
tool->input dataset recognition.
Should the problem be unrelated to file format, please send in a link to
a shared history (on the public Main server) and we can help to
troubleshoot from there. You can send this directly to me. From the
history panel use: Options (gear icon) -> Share or Publish -> generate
link -> copy/paste into email.
Best,
Jen
Galaxy team
On 11/22/12 3:16 AM, Jacqui Stockley wrote:
Hi,
I was wondering if you could help me with a problem I have been having
recently. I have carried out a number of NGS analyses using SAM Tools
where I have generated pileup and then filtered this file using the
filter pileup tool. However, recently when I have tried to do this the
filter pileup is not recognising a compatible dataset in the history
(ie it is not recognising the generate pileup file). I have always
done the same so I can't understand what I might have done wrong. I
have gone into old datasets and tried to filter pileups from previous
histories and they also do not recognise the generate pileup file
despite the fact they have previously!
Is there something I am doing majorly wrong or should I be using
another function?
Many thanks for any help or advice!
Jacqui
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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