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I am working with Illumina GAII derived mate pair data. I am attempting to identify two things in the sequences so that I can get rid of spurious data:
1. Are the reads rf or fr. I know picard must have the ability to identify this info from a sam as it provides such output when running the ColleceInsertSize... However, the output format is not what I need. Is there another tool that can provide rf/fr data for reads or is there a way to extract it from the sam?
2. Chimeric sequences. Not even sure where to begin here.
1. Are the reads rf or fr. I know picard must have the ability to identify this info from a sam as it provides such output when running the ColleceInsertSize... However, the output format is not what I need. Is there another tool that can provide rf/fr data for reads or is there a way to extract it from the sam?
2. Chimeric sequences. Not even sure where to begin here.