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@ccmiller2018
ccmiller2018 / chat.sh
Created March 19, 2023 20:13
This gist gives you a great starting place to chat with ChatGPT on the command line
#!/bin/bash
# Check if input string is provided
if [ -z "$1" ]
then
echo "Please provide a string input";
exit 1;
fi
# Tell the user i am thinking
@BenLangmead
BenLangmead / sra_growth.R
Last active September 23, 2024 09:00
SRA growth calc
system('curl https://trace.ncbi.nlm.nih.gov/Traces/sra/sra_stat.cgi > /tmp/stats.csv')
st <- read.table('/tmp/stats.csv', sep=',', header=T)
st$date <- as.Date(st$date, format='%m/%d/%Y')
i <- min(which(st$bases >= 0.5625e16))
id1 <- i
id2 <- min(which(st$bases >= 1.125e16))
id3 <- min(which(st$bases >= 2.25e16))
id4 <- min(which(st$bases >= 4.5e16))
id5 <- min(which(st$bases >= 8.95e16))
plot(st$date[id1:id5], log10(st$bases[id1:id5]), type='l', xlab="Date", ylab="log10(Total SRA bases)")
@andy-thomason
andy-thomason / Genomics_A_Programmers_Guide.md
Created May 14, 2019 13:32
Genomics a programmers introduction

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

@hlorand
hlorand / vidstab_ffmpeg.md
Last active October 3, 2024 05:18
Video stabilization using VidStab and FFMPEG

Video stabilization using VidStab and FFMPEG

** Step 1 **

Install ffmpeg with the vidstab plugin.

@lh3
lh3 / fq_download.md
Last active December 30, 2017 22:22
Downloading gzip'd fastq
Source Dst. file type Protocol Time (s) Command Line
NCBI .sra ftp 296 wget
NCBI .fastq.gz sra toolkit ~23000 fastq-dump -Z --gzip --split-spot
local file sra=>fastq.gz sra toolkit ~15000 fastq-dump --gzip --split-spot --split-3
EBI .fastq.gz aspera 513+492 aspera -QT -l 300m
EBI .fastq.gz ftp 1876+1946 wget

Notes:

@alyssafrazee
alyssafrazee / rnaseq.md
Last active September 22, 2023 01:11
rna-seq workflow (draft)

Analyzing RNA-seq data with the "Tuxedo" tools

Introduction/tl;dr: I wrote this post as a reference for a few new graduate students in my department that are getting started with RNA-seq data analysis. It begins with an informal, big-picture overview of RNA-seq data analysis, and the general flow of the post outlines one standard RNA-seq workflow, but I wanted to give general audiences a "heads-up" that the post goes into quite a bit of nitty gritty detail that's specific to our department's computing setup.

preliminaries: what's RNA-seq?

RNA-seq is a high-throughput technology used to measure gene expression in cell populations. For a super bare-bones picture of what gene expression is, please enjoy this ASCII art I made to illustrate the process:

[DNA]            ACGTAGGT{CGTATTT}AGCGT{AGCGCCCGA}TTACA
                                    |                   
@def
def / output
Created January 27, 2012 11:38
cPickle vs cPickle+HIGHEST_PROTOCOL vs marshal
cPickle default dumps: 0.107237100601
cPickle HIGHEST_PROTOCOL dumps: 0.0678668022156
marshal dumps: 0.0203359127045
cPickle default loads: 0.0411729812622
cPickle HIGHEST_PROTOCOL loads: 0.0352649688721
marshal loads: 0.0221829414368
@marcetcheverry
marcetcheverry / mapread.c
Created May 25, 2011 14:05
mmap and read/write string to file
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <fcntl.h>
#include <sys/stat.h>
#include <sys/mman.h>
#include <unistd.h>
int main(int argc, const char *argv[])
{