Nature Protocols · 2014 · 179 citations · 43 references
Life SciencesBiologyMolecular BiologyGene ExpressionGenomicsTranscriptomicsNext-generation SequencingNucleic Acid SequencingRna Sequencing AnalysisTranscriptomic ProfilingHigh-throughput Sequencing AnalysisRna SequencingRna Sequencing (Rna-seq)Targeted Capture SequencingTranscriptome Sequencing
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The Sequence Alignment/Map format and SAMtools
Heng Li, Alec Wysoker, Tim Fennell et al. · Bioinformatics · 2009 · 67.5K citations · Full text
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
STAR: ultrafast universal RNA-seq aligner
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BEDTools: a flexible suite of utilities for comparing genomic features
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An integrated encyclopedia of DNA elements in the human genome