Preprocessing workflow issues and comments

[Gregory94]

Place issues, comments and ideas here regarding the preprocessing using the workflow in Linux.

[Gregory94]

The initial version of the preprocessing workflow didn't allow for paired-end sequencing reads. This is now updated with a new version of the processing_workflow.sh bash file that can handle paired end sequencing data. A user can now select whether a single read sequencing file or paired-end sequencing files are used.
This is tested using a random small paired end sequencing file and that works fine, but I have not tested this workflow with a large paired-end sequencing file from S. Cerevisiae.

For the ones that are starting to use the Linux virtual machine, the version that is in the N-drive/VirtualMachines folder has already been updated with the newest workflow (read here to get started).
For anyone who already has a copy of the virtual machine you can update the workflow by copying the bash file to the shared folder of your virtual machine and in the terminal of the virtual machine enter the line cp /media/sf_sf_VMSharedFolder_Ubuntu64_1/processing_workflow.sh ~/processing_workflow.sh.

When you run in any problem, leave a comment in this issue.

[leilaicruz]

@Gregory94 ,once you have enough knowledge about , write here your take home messages about demultiplexing the data , an important step in our preprocessing analysis:

• good practices
• good tools
• experiences
• what you wont do again