> I have one more question about the "Anchor length". For a RNA-seq read mapped 
> on the splicing junction under the 0 mismatch condition, if 5 nucleotides of 
> one end map on one exon, does it mean the rest part of the read must map on 
> the adjacent exon? What I want to understand is that, although reducing 
> "Anchor length" may reduce the reliability of mapping on one end/exon, but 
> the increased number of mapped nucleotides on the adjacent exon may increase 
> the reliability of mapping. Does it mean overall the reliability of mapping 
> is not changed?

No, in general the probability of mapping 5 bases + (N-5) remaining bases 
incorrectly is higher than mapping 8 bases + (N-8) bases incorrectly because 
(a) there are more matching 5-mers than 8-mers in a genome and (b) there can 
mismatches when mapping the remainder.


The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to