Gene Means

It is often useful to reduce a combined_wig file (with insertion counts at each TA site) to a summary of mean counts for each gene in each condition, which can be done with the ‘gene_means’ command (in console mode), or by the following sequence of menu items in the GUI: ‘Pre-processing’->’Generate’->’Gene Means’.

By default, the gene means are calculated for each individual sample (column) in the combined_wig file. However, if desired, the user can request that counts be averaged over replicates of each condition (as defined in the metadata file), by including the ‘-cond’ flag. When averaging replicates together, gene_means uses TTR normalization by default.

Usage:
   > python3 /pacific/home/ioerger/transit/src/transit.py  gene_means <combined_wig> <metadata_file> <annotation_file> <output_file> [Optional Arguments]

   Optional Arguments:
   --n <string> :=  Normalization method. Default: --n TTR
   --iN <N>     :=  Ignore TAs within given percentage (e.g. 5) of N terminus. Default: --iN 0
   --iC <N>     :=  Ignore TAs within given percentage (e.g. 5) of C terminus. Default: --iC 0
   -cond        :=  Averages counts over replicates of each condition

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