Hi,
I have exome sequencing data in zipped fastq format that I am trying to align to the reference using CASAVA. My samples have been sequenced using illumina HiSeq2000 machine, 2 x 100bp paired-end sequencing. The first step in aligning the reads using CASAVA is that I need to create a configureAlignment configuration file. This is my first time using CASAVA so I am not sure how to do that. I was wondering if there is a default setting to align the read to the reference? How to pick what options to use? Can someone provide a sample config.txt file ?
Thanks for your input
I have exome sequencing data in zipped fastq format that I am trying to align to the reference using CASAVA. My samples have been sequenced using illumina HiSeq2000 machine, 2 x 100bp paired-end sequencing. The first step in aligning the reads using CASAVA is that I need to create a configureAlignment configuration file. This is my first time using CASAVA so I am not sure how to do that. I was wondering if there is a default setting to align the read to the reference? How to pick what options to use? Can someone provide a sample config.txt file ?
Thanks for your input
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