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454 adapter trimming alignment annotation assembly atac-seq bam bioanalyzer bioinformatics blast bowtie bowtie2 breakdancer bwa bwa sampe chip-seq cluster density cnvnator coverage cuffcompare cuffdiff cufflinks cuffmerge cuffnorm cummerbund cutadapt de novo assembly deseq dexseq dindel edger error fastq fastqc fpkm gatk htseq-count igv illumina ion torrent junction search failed metagenomics mirna miseq newbler nextera ngs normalization pacbio picard pindel prep_reads rna-seq rnaseq rpkm samtools samtools mpileup sanger/illumina 1.9 segmentation fault snp soap solid strand-specific tophat tophat segment junction truseq varscan vcf vcftools velvet

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