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  • 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.

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