Sequencing Data Organization Update


I’ve created a skeleton directory structure and included a few example folders so that everyone can get a better idea of how our data will be organized on the new sever. These are not set in stone. A few people have commented on the blog, or in lab meeting, or to me in person, and I’ve taken all of your suggestions into account.

If you feel like the setup here isn’t optimal, please give some feedback. The better we do this now, the more smoothly things will run in the future!

Using RSEM to estimate gene and isoform expression (Sam)

RSEM is a relatively new bioinformatics tool that has been developed in conjunction with Trinity for the analysis of RNAseq data. RSEM can be used to estimate expression levels for both genes and different isoforms of genes, and is quite quick and easy to use, with an excellent google group for help (“RSEM users”). All it requires is an RNAseq dataset (either fasta or fq format) and a reference transcriptome that it can be aligned to.

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