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Forum: Bioinformatics 08-02-2014, 11:50 AM
Replies: 17
Views: 5,540
Posted By Brian Bushnell
BWA-mem produces 'chimeric alignments'. This is...

BWA-mem produces 'chimeric alignments'. This is actually a really neat feature in some cases, and a big pain in other cases - in my opinion, it should be disabled by default.

If you look at the...
Forum: Bioinformatics 08-02-2014, 10:41 AM
Replies: 17
Views: 5,540
Posted By Brian Bushnell
The problem seemed to be caused by reads that...

The problem seemed to be caused by reads that magically appeared during mapping, and that normally means reads with multiple alignments. And short, extreme-GC reads are much more likely to map in...
Forum: Bioinformatics 08-01-2014, 08:54 PM
Replies: 17
Views: 5,540
Posted By Brian Bushnell
Great, looks like the problem is solved!

Great, looks like the problem is solved!
Forum: Bioinformatics 08-01-2014, 03:51 PM
Replies: 17
Views: 5,540
Posted By Brian Bushnell
If you are aligning with BWA, it now generates...

If you are aligning with BWA, it now generates "chimeric" alignments that you can't get rid of just by filtering for primary; you also have to exclude reads with flag "0x800". I suggest you look for...
Forum: Bioinformatics 08-01-2014, 12:51 PM
Replies: 17
Views: 5,540
Posted By Brian Bushnell
Before mapping, there appear to be ~zero reads...

Before mapping, there appear to be ~zero reads with 0% GC. After mapping, there are over 100,000. Those numbers are inconsistent. The primary peak centered on 20% GC appeared to stay the same...
Forum: Bioinformatics 08-01-2014, 12:25 PM
Replies: 17
Views: 5,540
Posted By Brian Bushnell
That contradicts your initial plot - for one...

That contradicts your initial plot - for one thing, there are more total reads after mapping.

Perhaps you have a few poly-AT reads and a few poly-AT regions in the genome, and you are generating a...
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