how to generate ini file

[cjose]

I've been given a csfasta and qual file to use in bioscope. I know that the ini file is set of instructions that uses the csfasta file. Is the ini file automatically generated somehow or do I make the file myself? I am trying to use the bioscope command line version which require the ini file for a plan file. Thanks in advance

[mapper]

If you use bioscope GUI for analysis .ini file will be generated automatically but if you want to run bioscope from command line , you need to create a ini file. ini is simple text file, you can use sample template of ini file and edit parameters in it and use it.

its nothing but just a list of parameters you want to use for analysis

[cjose]

All templates are different regarding the ones I have checked. What are the most basic file parameters I need to run bioscope? I know I need a reference, and a csfasta/qual file. Can i put two csfasta/qual files? Do I need a cmap? Just want to get this working.

[mapper]

yes there are diff templates for diff workflows. You dont need cmap file for all applications. cmap file is required when you want to run pipeline like indel finding/ CNV analysis...

There are few 'must define' parameters which should be there for bioscope to work. You need to define global parameters, pipeline name, reads/csfasta file and ref file.

Details of all parameters for each pipeline is provided in bioscope user guide. I would recommend you to look at it.

[cjose]

Thanks a lot - much appreciated.