Review RNASeqAnalysis plugin run results
- In the Data tab, click Completed Runs & Reports, then click the Report Name link for your completed sequencing run.
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In the list of runs, find the run of interest, then click the link in the Report Name column.
Reports for any plugins that have completed analysis are included in the Summary.
- In the left navigation menu, click RNASeqAnalysis to view the plugin results.
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In the RNASeqAnalysis section, view the Barcode Summary for the RNASeqAnalysis plugin. The summary includes columns for Barcode Name, Sample, Total Reads, Aligned Reads, Percent Aligned, Mean Read Length, Genes Detected, and Isoforms Detected.
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Click the RNASeqAnalysis.html link to open the report in the browser tab.
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Click the RNASeqAnalysis.html link to view the RNASeqAnalysis Report for all barcodes.
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Click the links at the bottom of the report to download associated report files:
Link name
Download description
A table that lists the sample name for each barcode, total reads, aligned reads and percent aligned.
A table that lists absolute reads for the genes found for each barcode.
A table that lists absolute normalized reads for the genes found for each barcode.
A table that lists the distribution of genes across barcodes to show the frequency of numbers of genes having similar log10 read counts.
The isoform gene heatmap in a table format.
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Click the links at the bottom of the RNASeqAnalysis Report to download raw analysis output files for the selected barcode. For examples, see Individual barcode view.
Link name
Raw analysis output file description
An overview of the individual barcodes from the RNASeqAnalysis plugin results.
A table that lists the number of times a gene was counted for the individual barcodes.
A directory for various output files for the selected barcode.
A list of links to Cuflinks output files.
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Click individual barcode names to see graphs for the selected barcode. For examples, see Downloadable reports for individual RNASeqAnalysis plugin barcodes.
Link name
Download description
A plot that shows the number of genes that have reads in log10 counting bins.
A summary of reads mapped to genes of the annotated reference.
A summary of base reads aligned to genetic features of an annotated reference.
A plot of normalized transcript coverage that shows the frequence of base reads with respect to the length of individual transcripts as they are aligned to in the 3" to 5" orientation.
Box plots showing variation of isoforms expressed at FPKM ≥ 0.3 for each set of genes grouped by the number of anticipated (annotated) isoforms. Whiskers are defined by points within Q1-1.5xIQR to Q3+1.5xIQR. Only genes with 25 or less isoforms are represented in this plot. The data and a plot for all genes are available for download using the download reports links at the bottom of the screen.
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Click the Distribution Plots, Correlation Heatmap, Correlation Plot, and Gene Heatmap tabs to review the following data graphically.
Graphical report
Description
Distribution Plots
For details, see Distribution plots.
Correlation Heatmap
For details, see Correlation heatmap.
Correlation Plot
For details, see Correlation plot.
Gene Heatmap
For details, see Gene heatmap.
Isoform Heatmap
For details, see Isoform heatmap.
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