The output from Tentacle is written to the output directory, which can be specified with --outputDirectory. The default output directory is called tentacle_output and will, after a finished run, contain two folders and one file:
[tentacle_output]$ ls
logs results run_summary.txt
The folder logs contains all the log files produced during the run, ready for inspection if something went wrong. The results folder will contain one file with results for each reads file (mapping job) in the run. The last file, run_summary.txt, contains an overview of all the jobs in the run.
The format of the output file that Tentacle produces is a tab separated text file with five fields: annotation, number of mapped reads, median number of mapped reads, mean number of mapped reads, standard deviation of mapped reads. The format is as follows (with TAB as separating character):
contig_annotation:startpos:endpos:strand count median mean stdev
[contig: string (no tabs or spaces) ] [int] [float] [float] [float]
[annotation: string (to tabs or spaces)]
[startpos: int ]
[endpos : int ]
[strand: + or - ]
This format is easy to parse and makes further analyses on. Since each reference sequence header (e.g. scaffold3_2) is separated with a _ before the annotation name (e.g. COGxxxxx) it is easy to separate the annotation name from the reference sequence header and extract further information like start and stop coordinates of the annotation. Statistics like number of mapped reads (count), median, mean, and standard deviation, of mapped reads to each annotated region of the reference are useful when making further analyses of the data.
An example of Tentacle output could look like this (with TABs instad of spaces):
scaffold3_2_COG3321:898:3862:+ 9 9.0 9.0 0.0
scaffold6_1_COG0112:0:570:+ 1 1.0 1.0 0.0
scaffold11_2_NOG08628:2:1589:- 8 8.0 8.0 0.0
scaffold13_1_COG0028:2:260:- 0 0.0 0.0 0.0
In this simple example the first COG3321 annotated region on scaffold3_2 has had 9 reads that mapped to it, for a median, mean and standard deviation of 9.0, 9.0, and 0.0, respectively.