3.Octopus-toolkit output directory

Octopus-toolkit creates five directories when you run the program.

  • Octopus-toolkit main directory.
_images/1.Main_folder.png
Main Folder Sub Folder Description
Index Reference, Hisat2, STAR Reference genome sequence and annotation files for analysis and alignment tools.
Log Command, Run Log file containing the commands used for analysis.
Result GSE_Folder, P_Folder The output files.
Script   Scripts used for analysis.
Tools Analysis tools Store the 3rd party tools used by Octopus-toolkit.

3-1.Index-Reference

  • Reference folder
_images/2.Reference_folder.png

The reference folder contains several reference files required for analysis.

Before starting each process, Octopus-toolkit checks the folder whether the reference files are prepared. If not, it automatically prepares the files.

3-2.Index-Hisat2

_images/3.Hisat2_folder.png

The reference genome sequence file should be indexed at least once before proceeding to the alignment step. The folder contains indexed genome sequence files used by the Hisat2 tool.

Octopus-toolkit inspects the index file of the genome before running the alignment process and runs the indexing step if it does not exist.

3-3.Log-Command

  • Command folder
_images/4.Command_folder.png

The Command directory contains log files containing the commands used during the analysis.

The file name adopts the date it is created. (2016_Dec_06.cmd.txt)

3-4.Log-Run

  • Run folder
_images/5.Run_folder.png

The Run directory contains log files containing running information recorded during analysis.

The file name adopts the date it is created. (2016_Dec_06.run.txt)

3-5.Result

  • Result folder
_images/6.Result_folder.png

The Result folder stores the output of Octopus-toolkit.

The folder name is based on the GEO accession number you entered. For the private data, the folder name begins with P_.

The Graph folder stores Heatmaps and Lineplots when you run the Graph function.

The detailed information regarding the output can be founded : Output Link

3-6.Script

  • Script folder
_images/7.Script_folder.png

The Script folder stores the script files used by Octopus-toolkit.

3-7.Tools

  • Tools folder
_images/8.Tools_folder.png

The Tools directory contains binary versions of 3rd party tools used in the Octopus-toolkit.