Mapping RNA-Seq reads for manual curation - FAQ

RNA-Seq reads mapped to your genome are essential evidence for manual curation of your genome. Here are some common questions that we get about RNA-Seq data.

What assembly should I map my RNA-Seq reads to?

• Your RNA-Seq reads need to be mapped to the genome assembly that we use to generate the browser.
• You can download the assembly under the "Current Genome Assembly" directory for your organism from our data downloads section: https://i5k.nal.usda.gov/content/data-downloads.

Should I trim my reads prior to mapping them?

• This is usually a good idea.

• CyVerse's learning center has a number of great tutorials for processing RNA-Seq data: https://learning.cyverse.org/en/latest/tutorials.html

Can you map my reads for me?

• Unfortunately, we don't have the capacity to do this.
• CyVerse's learning center has a number of great tutorials for processing RNA-Seq data: https://learning.cyverse.org/en/latest/tutorials.html

I've mapped my reads - how do I get the files to you?

• Great! Please contact i5k@ars.usda.gov to figure out the best way to transfer your files.

My mapped RNA-Seq reads are now available in Jbrowse, but I get an error when I try to view them. What does this mean?

• This usually occurs when there are too many reads aligned to the region to display properly. We can tweak some settings for you to visualize the reads, but this may make your browser slower or crash. If you are not particularly interested in the expression level of that area, and only want to visualize where genes are expressed, we can reduce the read coverage for you to a manageable level. Contact us if you're interested: https://i5k.nal.usda.gov/contact

What are the best files to display for manual curation?

• We recommend making the aligned reads (usually in bam format) and a gff or bed file of predicted splice junctions available.
• We can generate a histogram track (bigwig format) of the aligned reads for you.

Will my RNA-Seq data remain private?

• No. Anyone with the URL to JBrowse will be able to see the alignments, and download them on a scaffold-by-scaffold basis.
• If you are uncomfortable this, you should upload your mapped reads client-side - contact us if you'd like to know how to do this: https://i5k.nal.usda.gov/contact.