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Congratulations for your successful run of your [[GotCloud]] Tutorial. Please see [[#Tutorial Inputs]] section to prepare your own input files for your sequence data. You will need to specify the FASTQ files associated with its sample names as explained. In addition, you will need to download the full reference and resource file across whole genome (the Tutorial contains only chr20 portion to make it compact) See [[#Alignment Configuration File]] section for the detailed information. Also, please refer to the original documentation of [[GotCloud]] for more detailed guide on installation beyond the scope of tutorial
Congratulations for your successful run of your [[GotCloud]] Tutorial. Please see [[#Tutorial Inputs]] section to prepare your own input files for your sequence data. You will need to specify the FASTQ files associated with its sample names as explained. In addition, you will need to download the full reference and resource file across whole genome (the Tutorial contains only chr20 portion to make it compact) See [[#Alignment Configuration File]] section for the detailed information. Also, please refer to the original documentation of [[GotCloud]] for more detailed guide on installation beyond the scope of tutorial
= Tutorial Inputs =
= Input Files for GotCloud Tutorial =
This section describes the input files needed for the GotCloud tutorial. You don't need to know this detail to run the tutorial, but if you're interested in understanding the structure of GotCloud pipeline and run with your own sample, this would be a good starting point
== Alignment Pipeline ==
== Alignment Pipeline ==
=== List of Input Files needed ===
The command-line inputs to the tutorial alignment pipeline are:
The command-line inputs to the tutorial alignment pipeline are:
# [[#Alignment Configuration File|Configuration File (--conf)]]
# [[#Alignment Configuration File|Configuration File (--conf)]]
