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Personal Notes on RNA-seq

1 Trimming

2 Mapping

2.1 STAR

The --outSAMstrandField intronMotif option adds an XS attribute to the spliced alignments in the BAM file, which is required by Cufflinks for unstranded RNA-seq data (Dobin and Gingeras 2015).

Dobin, Alexander, and Thomas R. Gingeras. 2015. “Mapping RNA-Seq Reads with STAR.” Current Protocols in Bioinformatics 51 (1): 11.14.1–19. https://doi.org/https://doi.org/10.1002/0471250953.bi1114s51.