First, double check the column order as described on the tool form,
using the "Cut" tool as needed to rearrange data. Next, double check
that the format is assigned correctly as interval and the columns
assigments are made correctly as well (both can be done by clicking
on pencil icon to "Edit Attributes").
This is propriety data, correct? So you may to contact their support
about versions that are known to work with common 3rd party bioinfo
tools such as Picard. They may have solutions if the above does not
work. Picard is picky, especially this tool.
Hopefully this works out, but write back if you still have problems
after trying the above.
On 10/7/13 4:15 AM, Johnathan
My name is Johnathan Cooper-Knock, I am a clinical fellow based
at the University of Sheffield, UK.
I am trying to use Galaxy for analysis of DNA sequencing
data and I have run into a problem. I am trying to run the
SAM/BAM Hybrid Selection Metrics step on Galaxy (part of the
Picard tools) but I can't find bait and target bed files that
Galaxy will accept. My library capture was performed using
the Aglilent All Exon V4 kit and I have uploaded the
'S03723314_Regions.bed' and 'S03723314_Covered.bed' files from
but Galaxy does not even seem to recognise them as options for
entry. Is this a formatting issue? Do you know where I can
get ready formatted files?
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