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Old 03-18-2011, 07:51 AM   #2
Junior Member
Location: Barcellona

Join Date: Feb 2011
Posts: 4

this is my config file.
I have not a sam file in the output, but only some sh script:,,,
I don't know what is the next step because, as i write you, it's sometimes hard to guess which parameter name in the schema stands for which in the BFAST programs.
A suggestion:
if you have any validation errors with eclipse don't worry, they're not preclude the running of bfast.
I am a beginner so i don't know if this can help you. I hope..
Anyway, this is the BASIC xml version to run it:
<?xml version="1.0" encoding="UTF-8"?>
<bfastConfig xmlns:xsi="" xsi:noNamespaceSchemaLocation="BfastConfig_5.xsd">
<numReadsPerFASTQ localalignSplit="20" matchSplit="20">20</numReadsPerFASTQ>

To add any parameter, you can inspire from XSD and from
If you solved it, please share your code.
Thanks a lot.
Vincenzo is offline   Reply With Quote