mmterpstra

Bee Pic

Intro

This should show if there is an added yield in trimming nugene data by bedfile containing the landing probes. This applies tree different workflows for comparision as listed below.

Compared workflows

Trimbybed
- bbduk trim linker(hisat has diffculties with unaligned ends)
- hisat align
- trimbybed

	#intro

	#This shows how to downsample a bam without returning to fastq state of the file...
	#pros: Fast
	#cons: Might have alignment artifacts/info from the bigger subpool (like better indel alignments). Worse then completely stripping alignment info and aligning the reads again.

	#how to use

	#create a config and edit the downsample fractions as seen below and run the samples or just remove the leading part and create one yourselfs.
	#parallelisation is done in a lazy way and shoud be fixed/checked.

	#!/usr/bin/env python3
	import sys, os, time, subprocess
	#use findnotfinished.py /path/to/jobsdir

	try:
	input_dir = sys.argv[1];
	except:
	print('Die cannot open dir')
	exit

	#!/usr/bin/perl

	use strict;
	use warnings;

	use Proc::Daemon;
	use Proc::PID::File;
	use Getopt::Long;
	use Log::Log4perl qw(:easy);
	use File::Basename;

	#!/usr/bin/perl
	use strict;
	use warnings;
	use Data::Dumper;
	#Needs samtools binary/picard jarfiles hardcoded in script
	my $use = <<"END1";
	Use $0 PICARDJAR FILE(s)
	Tries to remove samplenames from bam/sam samplenames are extracted from SM field in header
	PICARDJAR Needs picard jarfile path in script
	FILE Needs *.bam

	#!/usr/bin/perl
	use warnings;
	use strict;
	use Data::Dumper;
	use Scalar::Util qw/ looks_like_number/ ;

	my $use = <<"END1";
	use
	$0 NUC LEN FASTA>BED
	Traverses the FASTA file and returns a BED file with the locations of the NUCleotide sequences spanning a length greather then or equal to LEN.

	set -e
	set -x
	set -o pipefail
	TMP00=./results/tmp/
	RAWDIR=/path/to/fastq/files
	ml picard/2.2.2-foss-2016a-Java-1.8.0_74

	(for fastq1 in ${RAWDIR}/*.fastq.gz; do
	echo "## INFO ##"$(date)" ## file '"$fastq1"' start"

	#!/usr/bin/perl
	use strict;
	use warnings;
	use Data::Dumper;

	my $use = <<"END";
	Simple extractor of the annotations between pre-defined regions in the gff format
	input
	perl $0 regions.gff ~/Downloads/Homo_sapiens.GRCh37.75.gtf > ~/regionsIntersectHomo_sapiens.GRCh37.75.gff
	no validation of input....