astatham

cat hg18.fa | awk '{
        if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")}
        print $0 > filename
}'

davidliwei

#!/usr/bin/env python
'''
Automatically estimate insert size of the paired-end reads for a given SAM/BAM file.
Usage: getinsertsize.py <SAM file> or samtools view <BAM file> | getinsertsize.py -
Author: Wei Li

Copyright (c) <2015> <Wei Li>

nathanhaigh

#!/bin/bash
# Usage: interleave_fastq.sh f.fastq r.fastq > interleaved.fastq
# 
# Interleaves the reads of two FASTQ files specified on the
# command line and outputs a single FASTQ file of STDOUT.
# 
# Can interleave 100 million paired reads (200 million total
# reads; a 2 x 22Gbyte files), in memory (/dev/shm), in 6m54s (414s)
# 
# Latest code: https://gist.github.com/4544979

wch

# =============================================
# Modifying a data frame in place
# =============================================

library(ggplot2)
str(diamonds)

# Modify data frame in place, in loop
# This is super, super slow
system.time({

Karel-Kroeze

# https://stackoverflow.com/a/45614547
GeomSplitViolin <- ggproto("GeomSplitViolin", GeomViolin, draw_group = function(self, data, ..., draw_quantiles = NULL){
  data <- transform(data, xminv = x - violinwidth * (x - xmin), xmaxv = x + violinwidth * (xmax - x))
  grp <- data[1,'group']
  newdata <- plyr::arrange(transform(data, x = if(grp%%2==1) xminv else xmaxv), if(grp%%2==1) y else -y)
  newdata <- rbind(newdata[1, ], newdata, newdata[nrow(newdata), ], newdata[1, ])
  newdata[c(1,nrow(newdata)-1,nrow(newdata)), 'x'] <- round(newdata[1, 'x']) 
  if (length(draw_quantiles) > 0 & !scales::zero_range(range(data$y))) {
    stopifnot(all(draw_quantiles >= 0), all(draw_quantiles <= 
                                              1))

benmarwick

# Adapted from https://stackoverflow.com/a/7267364/1036500 by Andrie de Vries

# This is it: theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

library(ggplot2)

td <- expand.grid(
  hjust=c(0, 0.5, 1),
  vjust=c(0, 0.5, 1),
  angle=c(0, 45, 90),

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.