The first step for your analysis is to get the data uploaded to the portal. All the workflows in this portal accept sequences in FASTQ format, either paired end (PE) reads or single end (SE) reads. For PE reads, you need to have two reads R1 and R2 in separate FASTQ files.

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To upload your data, please first login to the web portal, click the “Get Data”, then “Upload File from your computer” link on left column, a new window will appear, where you can drag and drop fastq files (see figure below).

• Please use gzipped fastq file for faster upload (uncompressed file is ok), gzip each individual fastq file.
• Please choose fastq as type (you can modify type later if you forget).

You can also upload your data to GenomeSpace and send it back to galaxy. Click the “Get Data” and then “GenomeSpace import from file browser”. You can see a new window of GenomeSpace. To do this, you need to register a GenomeSpace account first and upload your data into it, then select the data you want to upload, and click “Send to Galaxy”. Tainted fate cast iron. You will go back to galaxy server and it may take a while to upload the data.

Most importantly, you can also upload large files (>2.0Gb) via our FTP server. If you are comfortable with Linux, you can access it through terminal like this.

$ftp 52.11.154.125 #Provide your galaxy email and password as Name and Password.

ftp> put PATH/TO/FastqFile uploaded-1.fastq

If you are not comfortable with Linux, then forget about it, since you can also log in by FileZilla and drag whatever you want to the ftp server. To do it, you need to first download FileZilla and it is free. Once you installed it in your computer, you can edit Site Manager to save our ftp server as one of your sites. Please make sure to set Timeout in seconds to “120” in Connection Settings and select “Only use plain FTP (insecure)” for Encryption, “Active” for Transfer mode.

Then Click “Connect” button and provide your password. Then you can log into FTP and drag the file from local site to remote site.

It is quite time-consuming if your files are extremely large. After the ftp transfer is over, you can log into our galaxy server to see the uploaded file in “Choose FTP file” and select the files submitted to galaxy.

After your file is submitted into galaxy, it will remove from FTP server.

Once the upload is completed, you will see them in your history at right column. Please hit the “Edit attributes” icon to add or modify the data. It is highly recommended to give your data a simple and meaningful name (e.g. “tissue1-replicate1-R1.fq”, “control-replicate-R1.fq” etc), avoiding using special characters.

Sometimes you may need to combine the reads from different lanes for each sample. You can use cat function in Linux, but you can also click “Text Manipulation”, and then “Concatenate datasets tail-to-head” to combines them.