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adapter trimming alignment annotation annovar assembly atac-seq bam bbmap bioanalyzer bioconductor bioinformatics blast bowtie bwa chip-seq cluster density covaris coverage cuffcompare cuffdiff cufflinks cuffmerge cummerbund deseq deseq2 differential expression edger error fastq fastqc fpkm gatk genome htseq-count illumina insert size install ion torrent mapping metagenomics mirna miseq newbler nextera nextseq ngs normalization pacbio pindel pipeline quality rna-seq rnaseq rumors sam samtools sanger/illumina 1.9 segmentation fault sequencing snp solid tophat tophat2 trimmomatic trinity truseq varscan vcf vcftools velvet

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