this is for holding javascript data
sr320 added cuffdiff to local repo
Not syncing - ignoring
over 9 years ago
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Cuffdiff2_heat-b-2014-12-20-22-27-15.4/*
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#methods-RNAseq
Total RNA was
isolated.. extracted using Tri-Reagent per manufacturer’s instruction. Potential DNA carry-over was removed from extracted RNA using the Turbo DNA-free treatment according to the manufacturer's instructions (Ambion). RNA quality, library preparation, and sequencing was performed by ***GENEWIZ***. Libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit according to the manufacturer’s protocol (including bar-coding for multiplexing). Samples were multiplexed where three samples were run in one lane for Illumina Hiseq **100 bp paired end sequencing**.
Quality trimming of resulting sequencing reads was performed using CLC Genomics Workbench v. 7.0 (CLC Bio, Germany) with the following parameters: quality limit = 0.05, number of ambiguous nucleotides < 2 on ends, reads shorter than 20 bp were removed, and Illumina PCR primers were removed.
