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
I have generated pileup and then filtered this file using the filter
tool. However, recently when I have tried to do this the filter pileup
not recognising a compatible dataset in the history (ie it is not
recognising the generate pileup file). I have always done the same so
can't understand what I might have done wrong. I have gone into old
and tried to filter pileups from previous histories and they also do
recognise the generate pileup file despite the fact they have
Is there something I am doing majorly wrong or should I be using
Many thanks for any help or advice!
The "NGS: SAM Tools -> Filter pileup" tool was corrected last
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),
clicking on the pencil icon for a dataset, then the tab "Datatype",
assigning "pileup" manually (don't forget to save). This will help
tool->input dataset recognition.
Should the problem be unrelated to file format, please send in a link
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.