This section provides the identifiers and notations used to report the analysis results
on this website.
It also provides a description of some parts of the analysis and
some comments that may help understand the results.
Analysis Procedure
- Trimming
Trimming was done using Trimmomatic
- Read Mapping
Read Mapping was done using Bowtie2 (Results have not yet been replicated using Tophat
- Trancript Assembly and Abundance Estimation
Transcript assembly and abundance estimation was done using Cufflinks
- Differential Analysis
Differential Analysis was performed using Cyber-T
- Analysis Explanation
The heatmap was produced based on non-normalized expression levels found in the file ribosomeExpressionFPKM.tsv
Expression levels in this file are reported using FPKM. The expression values found in ribosomeExpressionFPKM.tsv
do not match the expression levels found in ribosomeNormalizedDifferentialExpression.tsv because the latter expression
levels have been normalized using VSN. This is also why some of the expression levels are reported as negative
The ribosomeNormalizedDifferentialExpression.tsv was filtered to only contain genes that are differentially expressed
with pVal < 0.5
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