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Salmon1 is a method for quantifying transcript abundance from raw read sequence fastq files, it will generate transcript level count matrix as output.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600148/
Running Count feature barcodes
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For more information about library file management, please see Library File Management.
References
Rob Patro, Geet Duggal, Michael Love, Rafeal A Irizarry, Carl Kingsford. Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference. Published online 2017 Mar 6. doi:10.1038/nmeth.4197
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