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I've mapped my reads - how do I get the files to you?
Great! Please contact firstname.lastname@example.org 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.
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.