In end-to-end mode, reads which map partially beyond the end of a reference sequence are discarded. For example, if there's a 100 base read and positions 11 to 100 in the read match the reference sequence's bases 1 to 90, then positions 1 to 10 of the read are beyond the reference sequence which causes the read to be discarded. If mapping was done in local mode, however, such reads might be kept. This is a problem when the RNA-seq assembly is incomplete or the database of transcripts only records the CDS sequence, omitting the UTRs.
In end-to-end mode, reads which map partially beyond the end of a reference sequence are discarded. For example, if there's a 100 base read and positions 11 to 100 in the read match the reference sequence's bases 1 to 90, then positions 1 to 10 of the read are beyond the reference sequence which causes the read to be discarded. If mapping was done in local mode, however, such reads might be kept. This is a problem when the RNA-seq assembly is incomplete or the database of transcripts only records the CDS sequence, omitting the UTRs.