For each annotation family including different repeat/Rfam families and other custom annotations, ncPRO-seq creates a table file showing read coverages of each single family member in all sequencing libraries. These table files are compatible with R package like DESeq [1] to identify significantly expressed family members. For instance, you can find read coverage of each miRNA gene in the miRNA table file. Note that in the tRNA table file, read coverages are computed based on types of tRNA instead of single tRNA genes, since several studies found that expressions of tRNA-derived small RNAs differ from one type of tRNA to another.
Chongjian Chen
2012-01-26
