I downloaded the transcriptome from a published paper where they sequenced the transcriptome from different organs of 2 different species of squid (squid U and squid E). Our lab recently sequenced the whole genome of Squid E. When I aligned the transcriptome of squid E from the previously published paper to its own genome, it aligns 80% (I used bowtie2 and hisat). However, the transcriptome of squid U processed the exact same way as squid E aligns only 1% or even less to the genome. The RNA was isolated and sequenced the exact same way in both the species and I processed them both the exact same way. Does anyone have theories why this might be the case?
This is the paper from which I used their transcriptomes: https://www.pnas.org/content/111/44/E4736.short
Did you align the sequencing reads, or the asembled transcriptome?
(I am assuming you tried to map the assembled transcriptome to a reference genome.) If squid U isn't very similar to squid E, bowtie2 and hisat aren't good tools for the job. You may try minimap2, gmap or spaln, they will do a better job for somewhat divergent species.