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gnarls 04-23-2015 02:03 PM

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`).

So BWA-SW, while aligning, broke the contigs into on average 5 or 6 pieces, is what I understand from that. I can visualize the alignments in IGV and they look good. What I'm trying to find out is: are there any sub-segments of those 60 contigs that were not successfully aligned to the reference genome I passed to BWA? In other words I have 339 sub-segments and I'm not sure if they fully constitute the 60 contigs I originally passed to BWA-SW.

I've searched for how to figure this out as best I can, but it seems like the majority of use cases for BWA are for aligning short reads, which is not what I'm doing at the moment. So I can find info on how to count unmapped reads but it doesn't seem to apply to my situation.


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