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

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