Jul
5
Best Practices for RNA-Seq
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The ENCODE Consortium has finalized Standards, Guidelines and Best Practices for RNA-Seq V1.0
RNA-Seq is a directed experimental approach aimed at characterizing transcription in biological samples. This document presents a set of guidelines and standards focused on best practices for creating ‘reference quality’ transcriptome measurements. As technologies are rapidly evolving and the aims of RNA-Seq experiments are diverse, this document does not cover all standards and quality control issues.
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30 M reads ??? PAIRED END ??? for differential espression analysis ? really is it the way you do it too ?
Talking with Illumina’s tech support they suggest 10 M 50 bp single reads for human / mammal transcriptoms and 50-100 M 2X75 or 2X100 bp reads for transcript analysis (splicing sites variants and trascripts’ mutations’ analysis