Finding genomic features from sequencing annotations

We will finalize this chapter and this book with a simple recipe that suggests that sometimes you can learn important things from simple unexpected results, and that apparent quality issues might mask important biological questions.

We will plot read depth (DP) across chromosome arm 2L for all the parents on our crosses. The recipe can be found on Chapter11/2L.ipynb.

 

 

How to do it…

1. Let's start with the usual imports:

%matplotlib inline

from collections import defaultdict
import gzip

import numpy as np
import matplotlib.pylab as plt

2. Let's load the data that we saved on the first recipe:

num_parents = 8
dp_2L = np.load(gzip.open('DP_2L.npy.gz', 'rb'))
print(dp_2L.shape)

3. And let's print median DP for the whole chromosome arm, and a part of it in the middle for all parents:

for i in range(num_parents):
    print(np.median(dp_2L[:,i]), np.median(dp_2L[50000:150000,i]))

Interestingly, the median for the whole chromosome sometimes does not hold for...