HandsFree FAQ

Sequence mapping on your fingertips. HandsFree.

HandsFree is a system designed by the Computational Medicine Center team at Thomas Jefferson University that allows other teams to take advantage of the developed mapping and analysis pipelines.
This system allows you to map and analyze RNA-Seq, Exome-seq, DNA-seq, and ChIP-Seq data to various reference genomes. It also automatically provides automatic post-mapping analysis such as gene expression normalization output and SNP detection.

Table of contents:
Is there a tutorial?
How can I demo the system?
What is my user name and password?
How do I change my password?
What sequencers are supported?
What reference genomes can I align to?
What input files can I process?
How to download and install FileZilla?
How to upload the input files and download the results?
How to configure the FTPS client?
What output does the pipeline generate?
How much does it cost to use HandsFree/How do I pay?
How can I upload my own sequence data?
Can I customize my jobs?
How can I check the status of my submitted job?
How long will my data be stored on your server?
Is any of the data backed up?
How to get help?

Is there a tutorial:
Yes, a step-by-step tutorial is located here.

How can I demo the system:
Upon registration, all users can demo the system using the SOLiD demo files (csfasta and qual file pair) that have automatically been deposited in each user's FTPS directory. In order to test-drive the demo files, you can do the following:

1. Log-in to HandsFree, then click 'New Job' at the top of the page
2. You can skip Step #1 as the DEMO files are automatically deposited in your FTPS directory
3. In Step #2, select both DEMO_ME_F3.csfasta and DEMO_ME_F3_QV.qual
4. Select the options you want for Step #3 (We used RNA/Human/Long for the demo, but you can choose other options if you want)
5. Select the options you want for Step #4
6. Submit the job when you are ready (Note: the demo files don't have many reads, its main purpose is to allow you to test-drive the system)

What is my user name and password:
Jefferson employees - For both the web and FTPS site, just use your regular campus-key userid and password.
Non-Jefferson users - For both the web and FTPS site, please use the user name (starting with 'ehf_') and password that you created upon registering for an account.

How do I change my password:
Jefferson employees: Click here
Non-Jefferson users:
1. Log out and go to the HandsFree home page.
2. Click the 'Forgot password?' button.
3. Enter your User Name beginning with 'ehf_'.
4. The system will confirm your user name and email you a token to reset your password.
5. Copy the password reset token from your email and paste it into the 'Password Reset Token' text field.
6. Once the token is confirmed, enter your new password and re-enter to confirm.
7. You will then receive an email confirming that your password has been changed.
8. Please be aware that you will need to restart the password reset process if you close the 'User Administration' window.

What sequencers are supported:
Ion Torrent, SOLiD, Illumina, and Solexa sequencers are supported. Please contact us if you want to request support for other sequencers.

What reference genomes can I align to:
We currently support the following genomes: Human (GRCh3a7) and Mouse (NCBIM37). Please contact us if you are interested in other genomes. .

What input files can I process:
Your input files must be transferred directly to the main root directory (the directory you automatically enter when you log-in via FileZilla).
1. For the SOLiD platform: the input file must have the XSQ format (newer machines), or include the [sequence file]_F3.csfasta and [sequence file]_F3_QV.qual file pair. If using a file pair, each file must be uploaded separately (don’t combine them together).
2. For Ion Torrent/Illumina/Solexa: the input file must be provided in .fastq or .fastq.gz (compressed) format. Solexa, Sanger, Illumina 1.3+, Illumina 1.5+, and Illumina 1.8+ phred formats are supported. The PHRED values in the FASTQ file must be in ASCII (non-Integer) format.

How to download and install FileZilla (required to transfer files to us via FTPS):
Please follow these instructions to download and install FileZilla on your computer.:
1. Visit the following site to download the installer: FileZilla Home Page.
2. Under 'Quick download links', select 'Download FileZilla Client - All platforms'.
3. Select the appropriate distribution for your operating system.
4. You will then be redirected to www.sourceforge.net.
5. You download should begin momentarily. If not click the direct link to download the installation package.
6. Finally, select 'Save File' and proceed to run the installer.

How to upload the input files and download the results:
In accordance to TJU/TJUH information security policy, you must send the input files to us via FTPS, not normal FTP. Likewise, you must use FTPS to download your results. In order to provide your input files, use FTPS to transfer them into the default directory. Click here to view the supported file types that you can upload.

How to configure the FTPS client:
Below includes detailed instructions on how to setup your FTPS FileZilla client. FTPS is different from both FTP and SFTP and the settings below are important for a successful connection into our service. Use the following settings to establish a secure FTPS connection to your home directory (Please note that all parameters are necessary to establish a secure connection):

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

Specific step-by-step instructions for FileZilla are as follows:
1. Open FileZilla.
2. If this is your first time connecting, then click the 'New Site' button on the Select Entry panel on the left side of the window. Give your connection a name such as 'TJU HandsFree'.
3. Select the Site Manager. This can be accomplished by clicking the Site Manager icon (the icon on the far left of the Toolbar), or by selecting File-->Site Manager on the application's Menu Bar.
4. On the first tab (General) enter the correct Host, Port, Protocol, Encryption, User (User Name) and Password provided above. Please click here for more information on your User name and passwork. The Logon Type should be 'Normal'.
5. Select the Transfer Settings tab and select 'Passive' from the Transfer Mode radio buttons.
6. Finally click the Connect button and you should be able to upload and download file from you home directory.

What output does the pipeline generate:
Please see this link for example output that the pipeline generates. Once you follow the link, the README file provides detail on what the output files are. In general, the output files are in various formats for your benefit, enabling you to work with your data in multiple ways (Excel, SAM tools, UCSC browser)

How much does it cost to use HandsFree/How do I pay:
Except for processing the demo files, you will be charged for each job submission. Before submitting your job, please double check all your job options.
For Ion Torrent:
1. For Single-Ended Reads (Academic pricing) : $10 per dataset
2. For Single-Ended Reads (Regular pricing) : $15 per dataset
3. Mate-Pair and Paired-End : availability and pricing will be coming shortly
For all other platforms:
1. For Single-Ended Reads (Academic pricing) : $177 for each 100 million raw reads given to us for analysis ($10 per dataset minimum cost per sample)
2. For Single-Ended Reads (Regular pricing) : $265 for each 100 million raw reads given to us for analysis ($15 per dataset minimum cost per sample)
3. Mate-Pair and Paired-End : availability and pricing will be coming shortly

The following step will be necessary to process your payment information:
1. Contact Christel Smith-Coleman at:
Email: Christel.Smith-Coleman@jefferson.edu
Phone: (215) 503-4219
Fax: (215) 503-0466
2. We will verify your payment information.
3. You will recieve a notification informing you that you have received full (read/write) access to the system.
4. You can then submit you job for mapping.
5. You will then receive an email with the cost to map/analyze your data.
6. This process will only take a few hours in total.

How can I upload my own sequence data:
Once your payment information has been received and verified, you will be able to upload your sequence data and download your mapped results. Click here for the contact information.

Can I customize my jobs:
Yes, various settings exist for you to customize your job. For example, you can optionally specify 5’ and 3’ adaptors to cut from your reads. Note, different options are presented reflecting the options you have chosen. For example, 'SNP detection' is only an option on DNA and not RNA.

How can I check the status of my submitted job:
Yes, multiple mechanisms are available to help you get the status of your job. You will receive an email both when your job starts processing and completes. Additionally, you can view the status of your job in real-time by going to the status dashboard.

How long will my data be stored on your server:
Once your job completes and our analysis is available, your input and output data will remain on our system for 30 days. Seven (7) days before the end of this 30-day period we will send you an automatic email to remind you to download your data to your own machines. A second reminder will be sent four (4) days and a third and final reminder one (1) day before the end of the 30-day period. If you fail to download your files during this 30-day period, they will be permanently deleted and there will be no way to retrieve them afterwards; the input data will need to be transfered to us again and any desired analyses will have to be rerun - this will incur new analysis charges.

Is any of the data backed up:
No, the data that you upload is not backed up on our systems. It’s very important that you maintain your own local copies of both input and output data at all times.

How to get help:
Please feel free to request help by contacting us.