Output

Format

The file contains full information about the normalized transcript/s. It consists of nine tab separated columns:

Column name	Description
transcript_id	ID of normalized transcript, the same as in the input file
position	Position in transcript
stops_treated	Stops count in the treated sample: from input counts file or calculated from BAM file
stops_control	Stops count in the control sample: from input counts file or calculated from BAM file
stops_norm_control	Normalized stops count in the control sample. Stops are normalized by incorporating the normalization factor (nf). Check The overview of probNORM method point B for more information
reactivity	Reactivity, calculated based on the normalized control stops. Check The overview of probNORM method point D for more information
fold_change	The ratio between stops counts in control and treated sample
p_value	P-value indicates the probability of nucleotide at a given position being a part of the background, not statistically significant. Check The overview of probNORM method point C for more information
passed_quality_filter	Quality filter (Y - yes / N - no). Transcript positions that exceed the filtering step are those with stops count higher than zero (both control and treated samples), without any missing parameters, and with proper coverage value (when a local script is determining the stops counts

probnorm counts -i example/counts-input.txt -o output.txt

transcript_id   position    stops_treated   stops_control   stops_norm_control  reactivity  fold_change p_value passed_quality_filter
RDN18-1 1   3095.0  3472.0  2669.1000000000004  1.0632124544542494  0.2135860512052699  0.37310634695017253 Y
RDN18-1 2   2029.0  1148.0  882.5250000000001   2.5274855472882036  1.2010598126290937  0.03438625350046609 Y
RDN18-1 3   315.0   360.0   276.75  0.09548691331973486 0.18676851160572655 0.38858771448505425 Y
RDN18-1 4   264.0   405.0   311.34375   0.0 -0.23797038886541122    0.6407954148840493  Y
RDN18-1 5   139.0   171.0   131.45625   0.018832141238058788    0.08050214738573189 0.45145693582080115 Y
...
RDN18-1 1776    0   0   0.0 0.0 0   0.5 N
RDN18-1 1777    0   0   0.0 0.0 0   0.5 N
RDN18-1 1778    0   0   0.0 0.0 0   0.5 N
RDN18-1 1779    0   0   0.0 0.0 0   0.5 N
RDN18-1 1780    25.0    9.0 6.91875 0.04513784971143676 1.8533447778805348  0.002490274610317811    Y

Summary information

After each use of probNORM the summary of run will be shown. It contains such informations as:

• input file type
• input and output file names
• parameters thresholds: coverage, p-value, reactive positions
• statictics about normalized transcripts

See the example below.

SUMMARY

BAM inputCOUNTS input

***** SUMMARY *****

    input mode: BAM
    input file/s: control: data/SRR955862_sort.sorted.bam treated:data/SRR955864_sort.sorted.bam
    output file: test.output
    min coverage: 0
    max p-value: 1.0
    min reactive positions per transcript: 20%
    selected transcripts:  all
    total number of input transcripts: 7127
    transcripts omitted due to low reactivity: 6887
    transcripts normalized: 240

*******************

***** SUMMARY *****

    input mode: COUNTS
    input file/s: data/counts-input.txt
    output file: test.output
    max p-value: 1.0
    min reactive positions per transcript: 20%
    total number of input transcripts: 2
    transcripts omitted due to low reactivity: 0
    transcripts normalized: 2

*******************