Counts format file

probNORM input file contains RT polymerase stops counts for both treated and control samples. The file consists of four tab-delimited columns:

1. Transcript ID

2. Position

3. Stops count in the control sample

4. Stops count in the treated sample

It is possible to upload multiple transcripts in one file. probNORM requires a minimum of 20 positions for each transcript to start the normalization process. At least 20% of those should have both control and treated counts higher than zero.

The example input counts file is provided in example/counts-input.txt

Options

To show full list of available options with their description type:

probnorm counts -h

Required

-i, --input

            The input file listing RT polymerase stops counts for both treated and control samples.
            The file structure is as follows: 1. Transcript ID; 2. Position; 3. Stops count in the control sample;
            4. Stops count in the treated sample;

-o, --output

            The name for the probNORM output file.

Optional

probNORM provides many additional parameters thet allow the detailed adjustment of the algorithm to the analyzed data.

-p, --pvalue

            P-value is the probability that a nucleotide belongs to the background distribution and is not statistically significant.
            Range [0-1]. All positions with a p-value higher than the provided one are rejected from the result.
            Default: 1 -> showing all positions.

-s, --transcript-size

            Set the percentage of transcript covered with reactive nucleotides. Those positions are further use to set normalization
            parameters. Default: 20 percent of provided transcript.

-f, --constrain-files

            The constrain files with normalized reactivities for RNAfold [ViennaRNA] and Fold [RNAStructure] will be prepared
            for each normalized transcript. Files will be saved in <output-file-name>_constrains.