Category: BINF 6215

BINF 6215: Taming Illumina datasets

BINF 6215: Taming Illumina datasets

As you’re uploading files to Galaxy or waiting for jobs to finish, you may be wondering “how can I make this go faster”? Scientists don’t like to throw out data, but Next Gen Sequencing...

BINF 6215: RNA-Seq in CLC Genomics

BINF 6215: RNA-Seq in CLC Genomics

OK — we’ve done a few exercises now where everything’s spelled out for you — this time you’re on your own.  You have access to a variety of bacterial RNA-Seq data sets. Legitimate things...

BINF 6215: Datasets

BINF 6215: Datasets

For practicing bioinformatics techniques in class, you can use any data set that’s not beyond the capacity of your computer. In practice that means that you probably want to use a bacterial NGS data set.

BINF 6215: Get your own Galaxy

BINF 6215: Get your own Galaxy

If you want to have some flexibility about what tools are available in your Galaxy instance, you can set up your own local instance. Remember that whatever you do with a local Galaxy instance...

BINF 6215: ChIP-Seq workflow in CLC

BINF 6215: ChIP-Seq workflow in CLC

On the first day of class, we downloaded a small ChIP-Seq data set and used it to practice using the SRA toolkit. Now we’re going to go back and analyze that.  Your first step...

BINF 6215: Intro to UNIX — automating a repetitive task

BINF 6215: Intro to UNIX — automating a repetitive task

Let’s say you’ve got a whole bunch of fastq.gz files that you want to get md5 checksums for so that you can upload them into the Short Read Archive. You could, of course, type “md5...

BINF 6215: Deposit your data in the SRA (Part 3: SRA Submission)

BINF 6215: Deposit your data in the SRA (Part 3: SRA Submission)

Step 3: Deposit data in the SRA. Now that you have your BioProject and BioSample identifiers, you are ready to deposit your data. You will need to create a username and password on the...

BINF 6215: Deposit your data in the SRA (Part 2: BioProject)

BINF 6215: Deposit your data in the SRA (Part 2: BioProject)

Step 2: Set up your BioProject Once you have your BioSamples set up, the next step is to create a BioProject.  First you’ll add your contact information.  For the class, we are going to...