Viewing Alignments


Exercises – Viewing Alignments

This is difficult to conceptualise so let’s get some hands on experience with a file containing aligned reads.

  1. Navigate to
  2. In the dropdown menu, select ‘Genome’, > ‘sacCer3’
  3. Navigate to the following web page:
  4. Download the two files RAP1_UNINDUCED_REP1.markdup.sorted.bam and RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai.
  5. In the dropdown menu, select ‘Tracks’ > ‘Local File’
  6. Upload the two files you downloaded, they are probably under downloads. Use the shift key to select both files at once.
  7. To see the reads, you need to zoom in on a gene. Type ‘chrI:87,174-87,813’ into the search bar to view the SCN1 gene.
  8. The histogram depicts the read coverage at the SCN1 gene. Scroll down in the interactive viewer to see the reads.

Bonus: there is a read with a green A highlighted – this is an example of a mismatch from the reference genome.

3. Data Analysis

Examples of data analysis that can be performed on RNA-Seq data will be provided in worksheets throughout the course.