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.