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Old 07-29-2015, 05:50 AM   #5
Nepher
Junior Member
 
Location: france

Join Date: Jan 2013
Posts: 4
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Thanks for your answer.

I came across a solution this morning. After checking lots of stuff I looked again at my reference sequence and I saw that there were special characters at the beginning of the sequence :

>name
??????ATCGTGCTA

I simply erased them and IGV removed the most part of mismatches (it left those from the mapping). I think that the mapping coordinates where simply shifted/reference sequence.

Hope this will help other users with IGV problems
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