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
run into a problem. I am trying to run the SAM/BAM Hybrid Selection
step on Galaxy (part of the Picard tools) but I can't find bait and
bed files that Galaxy will accept. My library capture was performed
the Aglilent All Exon V4 kit and I have uploaded the
'S03723314_Regions.bed' and 'S03723314_Covered.bed' files from '
https://earray.chem.agilent.com/suredesign/search.htm' but Galaxy does
even seem to recognise them as options for entry. Is this a
issue? Do you know where I can get ready formatted files?
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.