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adapter trimming alignment annovar assembly atac-seq bam bioanalyzer bowtie bwa bwa-mem bwa sampe chip-seq cluster density cnvnator covaris coverage cuffdiff cufflinks cuffmerge cummerbund cutadapt de novo assembly deseq dexseq edger exome fastq fastqc fpkm gatk htseq-count illumina ion torrent junction search failed library preparation metagenomics mirna miseq mpileup multiplex newbler nextera nextseq normalization pacbio picard pindel prep_reads quality rna-seq rnaseq rpkm sam samtools samtools mpileup sanger/illumina 1.9 segmentation fault snp soap solid sra strand-specific tophat tophat2 trinity truseq varscan vcf vcftools velvet


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