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dateformat	4

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

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

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#!/bin/bash

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

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

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Zasha Weinberg is looking for a PhD candidate in RNA bioinformatics

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#!/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> }

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