how does mim-tRNAseq handle partially mapped tRNA sequence?

[lkong888]

Hi, thanks for this great tool for tRNA analysis. I wonder how does mim-tRNAseq handle partially mapped tRNA fragment? And does mim-tRNAseq count pre-tRNA as mature tRNA? In the case of pre-tRNA, there will be either tailer or header sequence. Will mim-tRNAseq clip those extra sequence and then consider it aligned? Or would it just discard those reads with extra leader or tailer sequence?

[drewjbeh]

Hi there.
mim-tRNAseq does not consider pre-tRNA right now. The reads are soft-clipped for alignment to an extent but this probably is not enough to allow pre-tRNA read alignment to mature tRNA references. For tRNA fragments the case is less clear. These would likely map to mature tRNA sequence. But because tRNAs are so short, you should be able to visually recognize a large number of reads coming from fragments. Many reads should represent full length tRNAs except where known modifications cause shorter reads. You can see how many reads represent full-length tRNA transcripts for example in Figure 3C of the original paper