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Old 09-21-2011, 11:14 PM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

This will be the result of having reads which could have been aligned to several different contigs. If you run the above command against all of them then the read will be assigned to the best alignment across all contigs.

If you run against just one contig then there will be reads which match well enough against that contig to be counted as a hit, but which matched better elsewhere and would have been reported there when searched against all of your contigs.

If you need to see consistency then you'd need to specify -m 1 as an option so that only reads with exactly one valid alignment would be reported, however this is a much more stringent search and your overall mapping efficiency would be reduced.
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