Quality Checks (QC) and filtering of NGS reads before further processing

Brajbio · 05-23-2011, 12:38 AM

Hi ,

I am working on the RNA-Seq workflow and i am using illumina reads.
I was wondering if i need to perform any kind of QC or read filtering before processing with Tophat tool in the pipeline.

I would like to know what are the different QC practices in use for reads generated from different platform (Illumina, Roche etc)

What type of QC/filter is required to maintain data quality of sequenced reads?
What type of QC does Bowtie & TopHat performs?

Thanks in advance for your valuable suggestions.

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05-23-2011, 12:38 AM	#1
Brajbio Member Location: India Join Date: Jun 2010 Posts: 20	Quality Checks (QC) and filtering of NGS reads before further processing Hi , I am working on the RNA-Seq workflow and i am using illumina reads. I was wondering if i need to perform any kind of QC or read filtering before processing with Tophat tool in the pipeline. I would like to know what are the different QC practices in use for reads generated from different platform (Illumina, Roche etc) What type of QC/filter is required to maintain data quality of sequenced reads? What type of QC does Bowtie & TopHat performs? Thanks in advance for your valuable suggestions.