Exercise

Exercise 4

(a) Get all the repeat features from chromosome 20:1-500k. Print out the name and position of each on the chromosome and the total number.

Hint: create a slice, retrieve repeat features on this slice

(b) Find which genomic region the RefSeq dna entry NM_000059.3 was mapped to. Print the name of the region and coordinates of the alignment on the genome as well as the name of the region and coordinates of the alignment on the RefSeq dna entry. Print the score and percentage identity for the alignment.

Hint: use DnaAlignFeatureAdaptor; use the core schema documentation as a guide to appropriate methods which correspond to columns in dna_align_feature table

A list of useful Feature methods is in the Appendix (see page Recap and Appendix).

 

Answer

Magali explains the answers to these questions in this 4 min video. You can download her sample scripts and outputs:

a) sample script and output

b) sample script and output