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Old 01-06-2011, 12:49 AM   #1
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Location: Europe

Join Date: Jan 2011
Posts: 5
Default Maq how to filter low coverage areas?

Hello everybody,

Im doing my first steps in NGS-bioinformatics and I find this forum very useful!

Im using Maq for mapping illumina GAII reads.

Does anybody know how can I filter areas with low coverage (e.g. <5 reads) *not for SNP calling*, i.e. low coverage of reads that were perfectly aligned?

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