Filtering Illumina Reads
Found 3 free book(s)
MiSeq System Guide - Illumina, Inc.
support.illumina.comsequencing cycles plus any Index Reads with MCS v2.3 or later. Additionally,run duration is basedon the version of MiSeqreagents you are using and any performance enhancing upgrades installedon your instrument. For expecteddurations and other specifications,visit the MiSeqSystem specifications page on the Illumina website.
Practical Guide to Interpreting RNA-seq Data
btep.ccr.cancer.govQC Metric Guidelines mRNA total RNA RNA Type(s) Coding Coding + non-coding RIN > 8 [low RIN = 3’ bias] > 8 Single-end vs Paired-end Paired-end Paired-end Recommended Sequencing Depth 10-20M PE reads 25-60M PE reads FastQC Q30 > 70% Q30 > 70% Percent Aligned to Reference > 70% > 65% Million Reads Aligned Reference > 7M PE reads (or > 14M reads) > …
limma Linear Models for Microarray and RNA-Seq Data User’s ...
www.bioconductor.orgFunctions for reading and pre-processing expression data from Illumina BeadChips were intro-duced in limma 3.0.0. See the case study in Section 17.3 for an example of these. Limma can also be used in conjunction with the vst or beadarray packages for pre-processing Illumina data.