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Old 10-17-2011, 10:31 AM   #11
skruglyak
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Location: San Diego

Join Date: Sep 2010
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Quote:
Originally Posted by maubp View Post
Thanks.

Apologies if I was unclear - I was trying to distinguish raw reads in SAM/BAM (all reads unaligned) from a finished assembly/mapping in SAM/BAM (where most of the reads are aligned).

Sorry if I still misunderstand... CASAVA produces FASTQ files (not unaligned BAMs). The only BAM files produced are post alignment.
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