BYOD Workshop

The Cancer Genomics Cloud team is hosting a “Bring Your Own Data” workshop focused on RNA Sequencing analysis.

The workshop will take place on Friday August 19th from 1 to 5pm at the Seven Bridges offices in Cambridge, MA. We hope that you can attend!

For this workshop we will be trying something different - call it a clinic: you’ll bring and analyze your own data.  We will demonstrate how to build and run a custom RNA-Seq analysis workflow in which we align your reads against a reference, obtain gene-level counts, and perform differential expression all on the CGC. At the conclusion, you’ll be able to extend your analysis to any other data, including TCGA.

REGISTRATION:

Registration is now closed but you can fill out this Google form to indicate whether you would like to attend future events from Seven Bridges.

LOCATION:

Seven Bridges office: The East Arcade Conference Center, 1 Main Street, Cambridge, MA.

 

COME PREPARED!

Please note that we are planning on using the hg19/GRCh37 reference genome with gene annotations from UCSC or the GRCh38 reference genome with gene annotations from Ensembl Release 84 Databases. We expect you to bring FASTQ files from 101-bp, paired-end Illumina RNA-Seq. If you would like to analyze data using a different reference genome or read lengths, please e-mail cgc@sbgenomics.com to coordinate. Please be sure that you upload your data beforehand.

BEFORE ATTENDING THE WORKSHOP YOU SHOULD:

  • Create an account by clicking 'login' in the top right corner of this page. We recommend using your NIH credentials (see the video introduction here).

  • Upload the reads you want to analyze (ignore this if using data provided by Seven Bridges).
     

QUESTIONS:

  • I don’t have my own data. Can I still attend?

    • Absolutely! We will have public datasets available, including the Cancer Cell Line Encyclopedia.

  • What tools will we be using?

    • We will help you use STAR, TopHat2, HTSeq, Cufflinks, and DESeq2.

  • Is there a fee to attend?

    • The workshop is free! Users can also obtain up to $1600 in pilot funds to analyze their data, so you will not incur costs while trying things out.  

  • I have RNA-Seq data, but I want to do something else with it (e.g., detect chimeric transcripts, perform de novo assembly). Can you accommodate that?

    • We have over 200 bioinformatics applications available on the platform, so there is a good chance we will be able to help you out towards the end of the session when other people are setting up their own analyses. Let us know which analyses you’d like to perform in the Google form!

  • I want to use a reference genome besides hg19/GRCh37 or GRCh38 because I have a particular question or my data is not derived from human. Will I be able to analyze this?

    • Yes, but the Cancer Genomics Cloud is optimized for human data analysis and so doesn’t have publicly available reference files for non-standard reference or non-human genomes. Please fill out the form and we will provide you with instructions for some steps you will need to take to be able to participate in the workshop.

  • I love this idea, but I don’t do RNA-Seq/don’t live near Cambridge. Can you come do a workshop near me on the topic I’m interested in?

    • We’d love to!  We have performed workshops outside Boston for interested groups before. If you have a topic or want us to visit an area near you, please e-mail us at cgc@sbgenomics.com. Responses from tropical locations that need workshops during Boston winters are particularly encouraged.

  • How can I find out more about how to use the CGC?

If you have any questions regarding the content of the workshop or questions while you are using the CGC, please don’t hesitate to contact the Seven Bridges team at cgc@sbgenomics.com.

We'll continue to update this page with additional information as the workshop draws near. Check back again for the latest details and resources.