aseetharam

Bootstrap: docker
From: ubuntu:22.04  # Ubuntu-based for compatibility with older GLIBC

%labels
    Author Geoffrey Lentner and Arun Seetharam
    Description "Apptainer image for NeuPIMs with Rocky 8, custom CMake, Conan 1.57.0"

%environment

	export LANG=C

aseetharam

BootStrap: docker
From: ubuntu:20.04

%help
    HiFiasm is a fast and accurate assembler designed for HiFi reads produced by PacBio.

%labels
    Maintainer Arun Seetharam
    Version 0.1

aseetharam

#!/bin/bash

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

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

GTF=gencode.vM30.annotation.gtf

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

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

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

# 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

## 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

## 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

#!/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-"