Short RNAs were profiled using the Truseq protocol from Illumina, using an 8-plex. The 8-plex was first split by barcode and the resulting FASTQ sequences trimmed of the 3' adapter sequence. Sequences with low quality base N were removed. Ribsomal RNA sequences were then removed using the rRNAdust program. Remaining reads were then mapped using BWA version is 0.5.9(r16) and multimappers were randomly assigned.
