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Old 04-27-2016, 06:14 AM   #5
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239

Originally Posted by fanli View Post
I'd guess it's the first of your hypotheses. You could try BLAST/BLAT on some of the unmapped reads to see what they hit...
Thank you fanli for your suggestion.
I used the Web BLAST interface on the first "polyA" and "ribo" unmapped reads using "Genome (all assemblies top level)" as database and default settings.
1/10 reads from "polyA" unmapped.sam gets "No significant similarity found", the other 9 reads had pretty good similaries on the full read or on part of the read.
1/10 reads from "ribo" unmapped.sam gets similaries and the 9 other gets "No significant similarity found".

Is "Genome (all assemblies top level)" not the whole genome, with missing non coding regions where my "ribo" reads match? Or do they contain too many sequencing errors?
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