Hello, I need to add an extra genomic DNA to a genome assembly. 40% of this DNA encodes transcript, 60% isn’t transcribed but contains various regulatory elements as well as big region of non-coding sequence without any known functions. Historically, numeration (and importantly annotation) of this DNA begins from +1 of transcript and as result promoter is located at the 3-prime end. This is circular DNA, so in vivo +1 site follows the promoter. However, it will be added as linear fragment and I wonder what will happened when bowtie will attempt to align reads which begin at the promoter region and span into the transcribed part? Will it still align part of a read to 5-prime end and another part to 3-prime end of this DNA and give low scoring, or it will discard a read entirely?
If you use
--local (assuming bowtie2 rather than bowtie 1) then you'll get partial alignments at one of the ends. Note that you will still see a decrease in coverage near the ends and you won't have reads with portions mapping to both ends of the contig. This is a case where
bwa mem might be preferable, since it also produces supplementary alignments (so it can align part to each end of the contig).