chrisamiller

TCGA-AB-2812   13 28608256 28608257 -  TCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAG
TCGA-AB-2825   13 28608217 28608218 -  CCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTATTCGTG
TCGA-AB-2830   13 28608242 28608243 -  ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG
TCGA-AB-2836   13 28608267 28608268 -  TTCTCTGAAATCAACGTAGAAGTACTCATTATC
TCGA-AB-2840   13 28608248 28608249 -  ATTTGAGATCATATTCAT
TCGA-AB-2844   13 28608214 28608215 -  TTACCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCT
TCGA-AB-2853   13 28608268 28608269 -  TCTCTGAAATCAACGTAG
TCGA-AB-2869   13 28608253 28608254 -  GATCATATTCATATTCTCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGA
TCGA-AB-2870   13 28608258 28608275 CATATTCATATTCTCTGA   GGGGTGGGGGGG
TCGA-AB-2871   13 28608262 28608263 -  TCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC

chrisamiller

$ Rscript shortTest.R
Loading required package: IRanges
Loading required package: methods
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

chrisamiller

#! /usr/bin/perl

use strict;
use warnings;
use FileHandle;

#arg 0 - copy number calls produced by varscan "copyCaller" step
#arg 1 - segments of LOH, which give a reliable centering estimate (optional)

if(!$ARGV[0])

chrisamiller

library(sciClone)
library(clonevol)
library(fishplot)

## read in the data - copy number
cn1 = read.table("tumor.cn",sep="\t",stringsAsFactors=F)
cn2 = read.table("relapse.cn",sep="\t",stringsAsFactors=F)
cn1 = cn1[,c(1,2,3,5)]
cn2 = cn2[,c(1,2,3,5)]
## read in vaf data

chrisamiller

LSF basics

Interactive Jobs

Let's get a job on an interactive blade

bsub -Is -M 2000000 -R 'select[mem>2000] rusage[mem=2000]' -n 1 -q docker-interactive -a 'docker(chrisamiller/docker-genomic-analysis)' /bin/bash

Let's notice some things:

1. all of our data volumes are mounted and accessible
2. tools that weren't previously there, are there now

chrisamiller

workflow WGBS {

  String Reference = "/gscmnt/gc2708/info/medseq/gc6118/sketkar/refdata/mouse/all_sequences.fa"

  String JobGroup
  String? TMPDIR
  String OutputDir
  String FinalLabel
  String uBam

chrisamiller

##Mar 13, 2015
##Some 'date-names' are aliases and map to more than one gene
#symbol date name
SEPT1 1-Sep
SEPT2	2-Sep
SEPT3	3-Sep
SEPT4	4-Sep
SEPT5	5-Sep
SEPT6	6-Sep
SEPT7	7-Sep

chrisamiller

#notes from the "bash tips and tricks" workshop

#there are two paths coming out of every command - stdout and stderr

#by default both write to the screen
date #output to stdout
date --asdf #error to stderr

#you can redirect stdout to a file
date >file.txt

chrisamiller

#!/bin/bash

#auto update the build time
grep -v "^Packaged:" sciClone/DESCRIPTION >zz
mv -f zz sciClone/DESCRIPTION
thedate=`date +"%F %r"`;
echo "Packaged: $thedate; cmiller" >>sciClone/DESCRIPTION


version=$(grep "Version" sciClone/DESCRIPTION | awk '{print $2}')

chrisamiller

library(edgeR);
library(gplots);
library(RColorBrewer);
library(tximport);

# takes three arguments - config file, transcript to gene table, and output directory

# config file specifies the samples to import, groupings, and paths to abundance.tsv files from kallisto
# groups should be either 0 or 1
# header: sample \t group \t /path/to/abundance.tsv