12 Matching Annotations
  1. Oct 2020
    1. o visualize the data in UCSC genome browser, clic

      Provide trainees with a long period here to look at ucsc and play with it (time permitting)

    2. Recovering exon info

      So we have the original exon list, and we have a list of exon IDs, and the exon IDs on their own aren't very useful, so, let's find the exons in the original file which match these exon IDs

    3. ount the number

      Q: Ok, given last file, how would we figure this out? anyone know it in excel?

    4. fall into that exon?

      Again, numbers may be diff, compare with students

    5. Find exons with the most SNPs

      Q: What datasets do you have? How would you could about figuring this out? what information would you use?

    6. Again open the UCSC Main - table brows

      go back and do it again! It's the same thing over again

    7. When the dataset is green

      I usually just open the dataset and discuss what an exon is (genomic region w/ annotation.)

    8. Now set the following parameters:

      i'll read the parameters, but, they can check against the tutorial to be sure they're doing the right variables.

    9. Rename your history

      This is such an important step! So easy for students to get lost in their histories, remind them that it's normal, it happens to us, and life will be so much easier if they name things well.

    10. Browse to your favourite

      everyone should be logged into usegalaxy.eu by now

    11. Background

      Users can read if they like, but, not very important. Some people just really want to know the science, even though it's not relevant to what you're doing, which is learning how to manipulate the galaxy ui

    12. We start with the question: In human chromosome 22, which exon has the highest number of single nucleotide polymorphisms (SNPs)?

      Important to note for students, that they understand this central question