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Question: Fwd: Exome Sequencing Analysis
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gravatar for Johnathan Cooper-Knock
5.1 years ago by
Johnathan Cooper-Knock • 10
Johnathan Cooper-Knock • 10 wrote:
Hello, 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 ' https://earray.chem.agilent.com/suredesign/search.htm' 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? Thanks Johnathan
galaxy • 1.1k views
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modified 5.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.1 years ago by Johnathan Cooper-Knock • 10
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gravatar for Jennifer Hillman Jackson
5.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Johnathan, 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. Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENT • link written 5.1 years ago by Jennifer Hillman Jackson ♦ 25k
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