NGS Count QC

Performs an explorative analysis of expression estimates derived by Next Generation Sequencing.

Options

Supported options are:

• featureLevel=<gene|transcript> default: gene — whether to display expression for genes or transcripts (gene_id or transcript_id in the gtf file). If this is set to gene, the expression values of the transcripts belonging to a gene will be summed up.
• geneColumn=<column name> default: gene_id — the column in the count file that holds the gene id, this column will be used to merge transcripts into genes
• useSigThresh=<true|false> default: true — whether features with an expression below a threshold should be considered absent
• sigThresh=<num> default: 25 — the expression above which a feature is considered absent. Make sure to adapt this to your type of expression value
• columnName=<name of the column in the input file that holds the expression counts>. If unset will try any of: multiMatchCounts, transcriptExpressionPosteriorEstimate, transcriptCountPosteriorEstimate, transcriptCount
• normMethod=<logMean|median|quantile|none> default: none — how to normalize counts across samples
• backgroundExpression=<num> default: 5 — additive constant that is added to the expression values before building ratios that are plotted in heatmaps

For further options determining appearance of plots etc. see Analysis Parameters.

Notes

All scatter plots are on a logarithmic scale. In order to display features that have as expression 0 or NA these features is assigned a random value. The random value is chosen to be between 25% and 75% of the smallest non-zero expression value in the data set.