Step #1 – Download and Install the free 'FileZilla Client'
FileZilla will allow you to transfer files between your machine and ours. Click here for installation instructions.
(FileZilla uses the FTPS protocol for secure file transfer - FTPS is different than FTP or SFTP).
Step #2 – Configure the FileZilla Site Manager - Step 1
To configure the client, click the 'Site Manager' icon circled in red below or select 'File' and then 'Site Manager' from the menu bar.
Next press the 'New Site' button. You must then give your connection a name. Once completed, proceed to the next step.
Step #3 – Configure the FileZilla Site Manager - Step 2
1. Host Name: cm.jefferson.edu
2. Port: 1100
3. Protocol: FTP - File Transfer Protocol
4. Encryption: Require implicit FTP over TLS
5. User: This is the user name that you obtained when you signed up with HandsFree (see also this FAQ section for more information)
6. Password: This is the password that you obtained when you signed up with HandsFree (see also this FAQ section for more information)
7. Transfer Mode: Passive
Once you have connected for the first time, you will be prompted to accept our digital certificate as one of your web browser's trusted sites. The certificate, issued by a Certificate Authority, is used to maintain an encrypted (https) connection.
Use FileZilla to transfer the file(s) that you want mapped to our machine. These are the files with the read information that your institution's sequencing facility generated. Deposit these files in the top directory (the one containing the DEMO_ME_F3 files).
Wait until the transfer completes, then close FileZilla. (The directory in the right panel whose name begins with your user name contains the output files that we will generate for you.)
Step #4 – Select the files to analyze and Create a new job
Log in to HandsFree and click ‘New Job’ at the top of the screen. Then choose the file type (in the below screenshot, we chose ‘CSFasta/Qual’). You will then see a list of all CSFasta/Qual files that you uploaded. Next, click the ‘Select’ button for each of the files in the pair. Note: You will only be able to select one input file (or 1 file pair) for each created Job.
Step #5 – Select Job Type
In this step, you will need to give your job a name. This will help you identify and remember what your job is. In addition, you need to specify the species and type of sequencing performed. In the screenshot below, we chose short RNA for a human sample.
Step #6 – Select Job Options
For this step, start by clicking the ‘Job Options’ button. This step allows you to change the default job options (such as changing the default adaptors to cut from the sequencer reads).
Step #7 – Submit Job and view results
After you hit the 'Submit Job' button, your dataset will be queued for processing. The 'Status Dashboard' page provides a real-time status update of your job.
When your job completes, the associated Select menu will contain a 'Download' link to your results. You will be notified by email when your job has completed.