Output from the Quantify QIAseq UPXome workflow
The Quantify QIAseq UPXome workflow generates the following outputs for each demultiplexed sample:
- The demultiplexed reads in the subfolder Reads
- A Gene Expression track (
) A track, in the folder Gene Expression, with gene expression annotations, including counts and expression values for each gene. Hovering the mouse over an individual annotation reveals a tooltip with the gene name, expression value and associated information. Further details about this track type can be found at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Expression_tracks.html.
- A Transcript Expression track () A track, in the folder Transcript Expression, with transcript expression annotations, including counts and expression values for each transcript. Hovering the mouse over an individual annotation reveals a tooltip with the transcript name, expression value and associated information.
- A trimming report in folder <well name>/QC & Reports See http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.html.
- An RNA-Seq report (
) See http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_report.html.
and the following single outputs for all the samples:
- A Demultiplex Reads report () A report summarizing the demultiplex step.
- A Combined report (
) summarizing the reports for the individual samples.
Note that the Combine Reports tool can be used to combine multiple reports, summarizing results to allow for quality checks across samples. See http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Combine_Reports.html for further details.
- an Expression browser for genes, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Expression_Browser.html.
- an Expression browser for transcripts, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Expression_Browser.html.
- a Heat Map in both the folders Gene Expression and Transcript Expression, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Heat_Map_RNA_Seq.html.
- a PCA Plot in both the folders Gene Expression and Transcript Expression.