Bee Pic
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#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. |
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#!/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 |
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#!/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; |
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#!/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 |
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#!/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. |
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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" |
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http://www.howtogeek.com/116032/how-to-encrypt-your-home-folder-after-installing-ubuntu/ |
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#!/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.... |
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