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Dataset A: Illumina paired-end

File URL:

https://tinyurl.com/3chwns49/illumina.bam

(For index URL, add .bai).

You should be familiar with this type of data by now, as it's what the earlier practical was all about. The data has 150bp paired-end reads and was generated on the Illumina Novaseq 6000 platform.

IGV hints

This is a good point to try a few options to get used to IGV.

  • For paired-end data, try the 'view as pairs' option. It can be found in the context menu, obtained by right-clicking anywhere on the track.

  • Try clicking on a read. What is all that info? Where does it come from?

  • Try moving around and zooming in/out.

  • If you don't like how reads are displayed, try 'collapsed', 'expanded', or 'squished' from the context menu. Which one do you like best?

Warning

A reminder that all data in this sightseeing tour is included strictly for training purposes - it is not publicly-available data. Please do not share outside this course. Contact me (Gavin Band) if you have any queries about this.

Questions

Can you find:

  • a heterozygous SNP? A homozygous SNP?
  • an INDEL (short insertion or deletion variant)?
  • a sequencing error?

When you're ready, move on to Dataset B.