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Old 05-21-2009, 12:43 AM   #1
seq_GA
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Location: Asiana

Join Date: Feb 2009
Posts: 124
Default MAQ output format

Hi,

Recently started using MAQ and need some help to interpret mapping output as we have been using eland in the past.

Generated the 'maq map -N', using N option in order to get the mismatch positions in the final output.
Generated the alignment results using 'maq mapview -N' to view the results. As the manual says, the position of mismatches should be displayed and which column corresponds to this?

Does it output as eland resulsts like 32AT2 which means the first 32 bases are exact matches with the reference, 33rd and 34th positions are mismatches and last 2 bases are exact matches. Is there anyway to get output like this using MAQ?

How to compare the mapping quality of eland and MAQ results?

Thanks.
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