Mapping of a de novo assembled transcriptome to a genome of relative species

Question

[seta]

Hi all,

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?

Thanks,
Seta

Answer 1

[Devon Ryan]

I wouldn't recommend bowtie2 for this sort of task. You'll probably have better luck with BBMap or bwa bwasw.

Answer 2

[h.mon]

Bowtie2 is not suitable, you can use several programs, two that I recall immediately are Spaln and GMAP. I like them, had good results with both.

[seta]

Your prompt responses would be really apprecited. I try the suggested programs. thanks