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Ian Sealy iansealy

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iansealy / star-wars-rebels.md
Last active March 19, 2017 08:15
Star Wars Rebels episodes

Star Wars Rebels

Season 1

  • 1 Spark of Rebellion (part 1)
  • 2 Spark of Rebellion (part 2)
  • 3 Droids in Distress
  • 4 Fighter Flight
  • 5 Rise of the Old Masters
  • 6 Breaking Ranks
@iansealy
iansealy / rnaseq-intergenic.md
Last active August 12, 2016 10:48
Tuxedo

RNA-Seq (including intergenic assembly)

These notes assume you are using bash.

Firstly, login to farm3-login and create a new directory in one of your Lustre directories and change into it. For example:

mkdir /lustre/scratch110/sanger/is1/kdm2aa
cd /lustre/scratch110/sanger/is1/kdm2aa
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iansealy / detct-bam-merge-4-to-1.md
Created April 1, 2016 09:14
Merge 4 DETCT lanes to 1

Merge 4 DETCT lanes to 1

Set environment variables representing the four lanes. For example:

run_lane1=19231_1; run_lane2=19231_2; run_lane3=19244_1; run_lane4=19244_2

Extract all the samples and tags:

@iansealy
iansealy / rnaseq.md
Last active March 21, 2017 21:14
RNA-Seq

RNA-Seq

These notes assume you have multiple lanes of sequencing.

These notes assume you are using bash.

Make sure your ~/.softwarerc file contains (at a minimum):

team31
@iansealy
iansealy / rnaseq.md
Last active March 21, 2017 21:14
RNA-Seq

RNA-Seq

These notes assume you have a single lane of sequencing.

These notes assume you are using bash.

Make sure your ~/.softwarerc file contains (at a minimum):

team31
@iansealy
iansealy / rewrite_tc_tags_randomly.pl
Created January 9, 2015 11:46
#!/usr/bin/env perl
# PODNAME: rewrite_tc_tags_randomly.pl
# ABSTRACT: Rewrite transcript counting read tags (in random fashion)
## Author : is1
## Maintainer : is1
## Created : 2014-09-19
use warnings;
@iansealy
iansealy / zv9-ens77-classification.bed
Created October 19, 2014 21:29
Zv9 Ensembl 77 base classification
This file has been truncated, but you can view the full file.
1 0 2286 promoter
1 2286 2799 internal
1 2799 5806 tss
1 5806 14961 internal
1 14961 16962 tss
1 16962 21248 internal
1 21248 22251 promoter
1 22251 24302 tss
1 24302 25628 internal
1 25628 27629 tss
@iansealy
iansealy / orca-setup.md
Last active November 13, 2015 21:00
Orca setup notes

Install

Burn ubuntu-14.04-desktop-amd64.iso to DVD and boot from it and choose "Try Ubuntu".

Run "GParted Partition Editor" and set up the following primary partitions:

/dev/sda1   ntfs    windows  92160 MiB /   90.00 GiB
/dev/sda2   ext2    boot      1024 MiB /    1.00 GiB
/dev/sda3 ext4 ubuntu 143360 MiB / 140.00 GiB
@iansealy
iansealy / clone-wars.md
Last active February 28, 2017 15:20
Star Wars: The Clone Wars episodes

Star Wars: The Clone Wars

Season 1: A Galaxy Divided (2008–2009)

  • 1 Ambush
  • 2 Rising Malevolence
  • 3 Shadow of Malevolence
  • 4 Destroy Malevolence
  • 5 Rookies
  • 6 Downfall of a Droid
@iansealy
iansealy / detct-bam-generation.md
Last active October 24, 2016 17:40
DETCT BAM generation

DETCT BAM generation

These notes assume you are using bash.

First set an environment variable representing the run/lane. For example:

run_lane=11869_2