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Old 04-19-2012, 12:47 AM   #5
Location: Scandinavia

Join Date: Dec 2009
Posts: 20

Originally Posted by kopi-o View Post
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:
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.
Thanks, kopi-o.

I'm doing RNA-seq analysis with SOLiD platform. I read people mentioned carry out quality filtering (someone also called it as pre-filtering) before mapping is recommended. However, not much about how to deal with SOLiD csfasta but Illumina and 454 reads.

Thanks for the information. It is useful!
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