Michael T. Wolfinger mtw

## PhD Advertisement.pdf

      
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              February 4, 2021 21:41
            
              
                2021-02-03 Two PhD positions @TBI

              
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## extract_pp.sh
#!/bin/bash
samtools=`which samtools`
bn=$(basename $1 .bam)

echo processing $bn
$samtools view -h -b -f99  $1 > $bn.flag99.bam
$samtools view -h -b -f147 $1 > $bn.flag147.bam
$samtools view -h -b -f163 $1 > $bn.flag163.bam
$samtools view -h -b -f83  $1 > $bn.flag83.bam

## gist:3927eaebad6192bca9dc26c9e7b339a0
#!/usr/bin/env perl6

# a minimal Stockholm alignment format parser that reads
# ONLY single-line alignments and dumps each sequence (without additional
# gap characters) to a file

use Grammar::Tracer;

grammar StockholmParser {
	token TOP { <header>+ <alignment> <consensus> <sep>? <.eol> }

## README
Zasha Weinberg is looking for a PhD candidate in RNA bioinformatics

## bam2fastq_cutadapt.sh
#!/bin/bash

cutadapt=`which cutadapt`
fastqc=`which fastqc`
bam2fastq=`which bam2fastq`
gzip=`which gzip`
origdir="."
results="cutadapt"
fastqcdir="${results}/FastQC"
adapter5="CTACACTCTTTCCCTACACGACGCTCTTCCGATCT"

## cuff_me.sh
#!/bin/bash
bamdir="./"
cufflinks=`which cufflinks`
annotation="foo.gtf"
threads=40
label_RABT="CUFFRABT"
label_denovo="CUFFDENOVO"

for BAM in $(ls $bamdir/*.bam)
do

## dsm.opt
dateformat	4

## dexseq_count_em.sh
#!/bin/bash
samdir="./"
dexseq_flat_gff="my.DEXSeq.gff"
outdir="./dexseq-count"
dexseq_count="python /home/foo/bin/dexseq_count.py"
samtools=`which samtools`

if ! [ -d "$outdir" ];
then
        mkdir -p $outdir

## cutadapt_em_PE.sh
#!/bin/bash

cutadapt=`which cutadapt`
fastqc=`which fastqc`
origdir=".."
results="."
fastqcdir="${results}/FastQC"
adapter5="CTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
adapter3="GATCGGAAGAGCACACGTCTGAACTCCAGTCAC"
inprefix="C"

## htseq_count_em.sh
#!/bin/bash
samdir="./"
annotation="my.gtf"
htseqdir="./htseq-count"
htseqcount=`which htseq-count`
samtools=`which samtools`
feature="gene"
idattr="gene_name"
ss="reverse"
	#!/bin/bash
	samtools=`which samtools`
	bn=$(basename $1 .bam)

	echo processing $bn
	$samtools view -h -b -f99 $1 > $bn.flag99.bam
	$samtools view -h -b -f147 $1 > $bn.flag147.bam
	$samtools view -h -b -f163 $1 > $bn.flag163.bam
	$samtools view -h -b -f83 $1 > $bn.flag83.bam
	#!/usr/bin/env perl6

	# a minimal Stockholm alignment format parser that reads
	# ONLY single-line alignments and dumps each sequence (without additional
	# gap characters) to a file

	use Grammar::Tracer;

	grammar StockholmParser {
	token TOP { <header>+ <alignment> <consensus> <sep>? <.eol> }
	#!/bin/bash

	cutadapt=`which cutadapt`
	fastqc=`which fastqc`
	bam2fastq=`which bam2fastq`
	gzip=`which gzip`
	origdir="."
	results="cutadapt"
	fastqcdir="${results}/FastQC"
	adapter5="CTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
	#!/bin/bash
	bamdir="./"
	cufflinks=`which cufflinks`
	annotation="foo.gtf"
	threads=40
	label_RABT="CUFFRABT"
	label_denovo="CUFFDENOVO"

	for BAM in $(ls $bamdir/*.bam)
	do
	#!/bin/bash
	samdir="./"
	dexseq_flat_gff="my.DEXSeq.gff"
	outdir="./dexseq-count"
	dexseq_count="python /home/foo/bin/dexseq_count.py"
	samtools=`which samtools`

	if ! [ -d "$outdir" ];
	then
	mkdir -p $outdir
	#!/bin/bash
	samdir="./"
	annotation="my.gtf"
	htseqdir="./htseq-count"
	htseqcount=`which htseq-count`
	samtools=`which samtools`
	feature="gene"
	idattr="gene_name"
	ss="reverse"