Comparing Novel RNA Sequences

Question

[ruchiksy]

Hello,

I have two .txt files. Both files contain data regarding splice junctions and I'd like to create a very simple bar graph to see the distribution of Novel RNA sequences. The splice junctions come out of two different mapping methods.

I have written some python code but am a novice so I am having some difficulty in debugging. Here is my code:

# This script will plot the comparison between the BodyMap Gencode & BodyMap RefSeq paired end data.

import matplotlib.pyplot as plt
import numpy as np


#Reading in the files

with open("Illumina_Heart_Gencode_Aligned_Novel_Junctions.txt") as f:
        data = f.read()

data = data.split('\n')

x = [row.split(' ')[0] for row in data]
y = [row.split(' ')[1] for row in data]

fig = plt.figure()

ax1 = fig.add_subplot(111)

ax1.set_title("BodyMap Gencode Vs. RefSeq")
ax1.set_xlabel("Novel & Splice Junctions")
ax1.set_ylabel("Something")

ax1.plot(x,y, c='r', label='the data')

leg = ax1.legend()

plt.show()

I'd like to read in the 6th and 7th columns from both text files for comparison, rest of the columns are immaterial. Could I receive some pointers?

Thank you,

[Rodrigo Goya]

You might want to provide more information on your original files. You mention two files but you are only reading in one in your code. You say you want columns 6 ad 7, but are they numbers? Strings? What do they represent? Is it junction expression? Is it the junction ID?