Unique mapping reads in RNA seq data analysis means what?

[khushal]

Unique mapping reads in RNA seq data analysis means what?

Basically a gene may have several transcripts called transcripts variants. Therefore, a read will be smaller that transcript for eg. 100 bp tanscript during sequencing generate 2 reads of equal 50 bp length length. This one read (50 bp) will align to more than ONE tanscript.

Unique mapping reads means what: should read strictly align with one transcript only or a read can align with more than one transcript belongs to one gene id/ ensembl id only ?

[wdecoster]

In general, this refers to mapping to the genome and not to the transcriptome. As such, reads mapping once in the genome are 'uniquely mapping'.