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Old 04-19-2012, 12:21 AM   #4
kopi-o
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Location: Stockholm, Sweden

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OK. So, pre-filtering (I would call it quality filtering) is distinct from duplicate removal and you can think of them as independent filtering steps.

For SOLiD specific quality filtering, and looking at the data in a somewhat similar way to FastQC, I have used this toolkit: http://hts.rutgers.edu/filter/
Then you don't need to convert to FASTQ.

For some types of analysis, you may not need to do quality filtering (e g ChIP-seq, RNA-seq). The bad reads will (in general) simply fail to map. For de novo assembly, or resequencing where variant calling is important, you should do quality filtering.
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