SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   General (http://seqanswers.com/forums/forumdisplay.php?f=16)
-   -   BWA-SW contig to reference -- what was unaligned? (http://seqanswers.com/forums/showthread.php?t=57927)

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.

Thanks....


All times are GMT -8. The time now is 05:04 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.