Alignment
to genome
Computationally
expensive
It is never
a good idea to simply align HTS data to the genome
Need a
spliced aligner or a surrogate (such as including exon-exon junction sequences in ‘genome’)
Alignment
to transcriptome
Reads
deriving from non-genic structures may be ‘forcibly’ (and erroneously) aligned to genes
Incorrect
gene expression values
False
positive SNVs
Many other
potential problems
Assembly
Low
expression = difficult/impossible to assemble
Misassemblies/fragmented
contigs due to repeats
Requires
vast amounts of memory