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Forum: General 04-23-2015, 02:03 PM
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Views: 1,791
Posted By gnarls
BWA-SW contig to reference -- what was unaligned?

I used BWA-SW to align 60 contigs to a reference genome. The resulting SAM file has 339 entries (I did `samtools view -c myfile.sam`). All of these are "mapped" (`samtools view -c -F 4 myfile.sam`). ...
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