A Practical Guide to Cancer Systems Biology

52 A Practical Guide to Cancer Systems Biology

Table 1. Common file formats for RNA-seq analysis

Format Description

FASTQ The FASTQ format stores sequences and qualities scores in a single file.
FASTQ file uses four lines per sequence:

• Line 1: begins with a “@” character and is followed by a sequence
  identifier with/without a sequence description


• Line 2: the raw sequence letters


• Line 3: begins with a “+” symbol


• Line 4: encodes the quality values for the sequence in Line 2

SAM/BAM SAM format data is the output from aligners that read FASTQ files and
assign the sequences to a position with respect to a known reference
genome. BAM stores the same data as SAM file in a compressed,
indexed, binary form. These two formats can easily convert to each
other using SAM tools
GTF/GFF The gene transfer format (GTF) and general feature format (GFF) are
the file format used to describe information about gene structure. GTF
is a tab-delimited text format based on GFF, but contains some
additional conventions specific to gene information.
BED BED format provides a flexible way to define the data lines that are
displayed in an annotation track
WIG The wiggle (WIG) format is for display of dense, continuous data such as
the coverage of mapped reads.

Create a galaxy account

As a registered user on the Galaxy main server, Galaxy will allow all the
work to persist between sessions.

1. In the masthead at the top of page, click the “Register” link under the
   “User”.


2. Provide your information to Galaxy by entering your valid email address,
   password, and confirm your password.


3. Your Galaxy account will be created by clicking the submit button.

Upload sequence data to galaxy

You can import data from your local storage either from a website or FTP
site, you can even retrieve data from different databases, such as EBI SRA
and UCSC via “Upload file” function.

1. In the Tools panel, expand “Get Data” and click “Upload file”.


2. Drag and drop files into the pop-up window, or click “Choose local file”
   to select the files from your local storage. If your files are from a website,
   click “Paste/Fetch data” and paste the URL into the text-entry box.