I have done a de novo transcriptome assembly, now I'm trying to map the assembled transcriptome (with 80,000 contig from 300-13000 bp in length) to a genome of relative species. This genome is also resolved at the scaffold level. I used bowtie2 after genome indexing using the command of "bowtie2 -f -U all_to_seq.fasta -p 4 -x cs --no-unal -S testcs.sam". However, the alignment rate is very low (0.01%).
Could you please let me know how I can improve the alignment rate?. Is bowtie2 suitable for this purpose?