aseetharam

"""==============================
Branded IPython Notebook Launcher
=================================

Executing this module will create an overlay over ipython notebooks own static
files and templates and overrides static files and templates and copies over all
example notebooks into a temporary folder and launches the ipython notebook server.

You can use this to offer an interactive tutorial for your library/framework/...

aseetharam

library(Heatplus)
library(vegan)
library(RColorBrewer)
library("gplots")
all.data <- read.csv("C:/Users/Arun Seetharam/OneDrive/PostDoc/Projects/20150303_Perera_metabolomics/bloodroot_data_v2d.csv", quote="")
row.names(all.data) <- all.data$ID
all.data <- all.data[, -1]
data.prop <- all.data/rowSums(all.data)
scaleyellowred <- colorRampPalette(c("lightyellow", "red"), space = "rgb")(100)
heatmap(as.matrix(data.prop), Rowv = NA, Colv = NA, col = scaleyellowred)

aseetharam

#!/bin/bash
num=1
while read line; do
start=$(echo $line |cut -f 1 -d ",");
end=$(echo $line |cut -f 2 -d ",");
strand=$(echo $line |cut -f 3 -d ",");
  if [ "$strand" = "+" ]; then
     echo -e "253771435\t$((start - 3))\t${start}\t${num}\t0\t+";
  else
     echo -e "253771435\t$((${end} - 1))\t$((${end} + 2))\t${num}\t0\t-"

aseetharam

## OPTION 1
# convert the gzipped fastq file to a single line sequence files
zcat input.fastq.gz | sed -n '2~4p' > single_line_sequences.txt
# you are aksing it to print 2nd line followed every 4th line after that.
perl -ne 'while ($_ =~ m/GTGTTCCCCGCGCCAGCGGGGATAAACC([ATCG]{32})/g) {print $1."\t"} {print "\n"}' single_line_sequences.txt
# here, you are printing the 32 bases after the matching string using perl and using tab as delimiter. 
# the input is the above file you created in the first step.
# this will generate the output for the first part.

## OPTION 2

aseetharam

## find the spacers
grep -one "GTGTTCCCCGCGCCAGCGGGGATAAACC.\{32\}" example.list | \
sed 's/:GTGTTCCCCGCGCCAGCGGGGATAAACC/\t/g'  | \
awk '{print ">"$1"\n"$2}' > example_spacers.fa
# find the crispr sequences, extract the 32 bases spacers adjacent to it and print them as fasta sequence
# multiple spacers from the same sequence are printed with the same sequence id
# to count:
grep -c ">" example_spacers.fa
# will give you total number of spacers
grep ">" example_spacers.fa |sort |uniq |wc -l

aseetharam

# here is an example to write seperate files based on number of occurences of spacers:
perl -ne 'while ($_ =~ m/GTGTTCCCCGCGCCAGCGGGGATAAACC([ATCG]{32})/g) {push(@matches, $1)}if(@matches){ print "@matches\t";undef @matches; print "\n"}' example.list | awk 'NF==2'
GGTAACTTGCCGGAGGGCAGCGACCAGTTTAA GATGCACAGCCTGTTGCCATTCCGCCTCCTGT
GCAACTCGGTCGCCGCATACACTATTCTCAGA GGAAAGCCTCTTTCCTTTGTTTACGATATTGC
GGTTTTGCGCCATTCGATGGTGTCCGGGATCT GCGGCCCACGCTGGTTTGCCCCAGCAGGCGAA
GCGCTGATTTCTTAATGTGATCGGTAGCACGT AAAAAATTATATTGACGCGGCGAGTTATAATA
GTGCTCCAGTGGCTTCTGTTTCTATCAGCTGT GGGTGAACACTATCCCATATCACCAGCTCACC
GGAATATTCAGCGATTTGCCCGAGCTTGCGAG GCGTGCCGCCCCCAGCAACAATACGCTACTGA

# see the last part (awk 'NF==2'), here you are specifying that the number of fields should be exactly 2, you can change this to 1 to-

aseetharam

canu \
   -d /project/rw_genome/arun_test/20170928_canu_c \
   -p 20170928_canu_c genomeSize=770m \
       maxMemory=128g \
	   maxThreads=16 \
	   gridOptionsJobName=canu_as1 \
	   gridOptionsExecutive="--mem-per-cpu=5g --time=2:00:00" \
	   gridOptionsCORMHAP="--mem-per-cpu=5g" \
	   gridOptionsCORMHAP="--time=1:00:00" \
	   gridOptionsOBTMHAP="--mem-per-cpu=5g --time=1:00:00" \

aseetharam

canu \
   -d /project/rw_genome/arun_test/20170928_canu_b \
   -p 20170928_canu_b \
      genomeSize=770m \
	  maxMemory=1096g \
	  maxThreads=40 \
	  minReadLength=1000 \
	  corOutCoverage=35 \
	  gridOptionsJobName=canu_as-b \
	  corMhapFilterThreshold=0.0000000002 \

aseetharam

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.

aseetharam

#!/bin/bash

BEDTOOLS=$(dirname $(which bedtools))
FEATURECOUNTS=$(which featureCounts)
R=$(which R)

IDIR=$(pwd)
DIR=$(pwd)/GeneBed_output

GTF=gencode.vM30.annotation.gtf