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adapter trimming alignment annovar assembly atac-seq bioanalyzer bowtie bowtie2 breakdancer bwa bwa-mem bwa sampe chip-seq cluster density cnvnator covaris coverage cuffcompare cuffdiff cufflinks cuffmerge cuffnorm cummerbund de novo assembly deseq dexseq dindel dwgsim edger error fastq fastqc fpkm galaxy gatk geneious hiseq htseq-count illumina insert size ion torrent junction search failed mirna miseq mpileup multiplexing newbler nextera novoalign pacbio picard pindel prep_reads rad sequencing rna-seq rnaseq rpkm samtools samtools mpileup sanger/illumina 1.9 segmentation fault soap strand-specific tophat tophat segment junction truseq varscan vcf vcftools velvet


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