ilevantis

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

darencard

Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.

Extracting paired FASTQ read data from a BAM mapping file

Sometimes FASTQ data is aligned to a reference and stored as a BAM file, instead of the normal FASTQ read files. This is okay, because it is possible to recreate raw FASTQ files based on the BAM file. The following outlines this process. The useful software samtools and bedtools are both required.

From each bam, we need to extract:

1. reads that mapped properly as pairs
2. reads that didn’t map properly as pairs (both didn’t map, or one didn’t map)

zaltoprofen

from sklearn.preprocessing import PolynomialFeatures
from sklearn.linear_model import LinearRegression, Lasso
from sklearn.pipeline import Pipeline
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats

modelF = lambda deg: Pipeline([
    ('poly', PolynomialFeatures(degree=deg)),
    ('linear', LinearRegression(fit_intercept=False))])

slowkow

#!/usr/bin/env python
"""
GTF.py
Kamil Slowikowski
December 24, 2013

Read GFF/GTF files. Works with gzip compressed files and pandas.

    http://useast.ensembl.org/info/website/upload/gff.html