mtw

mtw

#!/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> }

mtw

Zasha Weinberg is looking for a PhD candidate in RNA bioinformatics

mtw

#!/bin/bash
chromsizes="./chrom.sizes"
genomeCoverageBed=`which genomeCoverageBed`
bedGraphToBigWig=`which bedGraphToBigWig`
vis="./vis"
samples=9
fromsample=1
rep=2
fromrep=1

mtw

#!/bin/bash

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

mtw

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

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

mtw

dateformat	4

mtw

#!/bin/bash

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

mtw

#!/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

mtw

#!/bin/bash

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