Question: Mapping of a de novo assembled transcriptome to a genome of relative species
0
gravatar for seta
3.4 years ago by
seta1.1k
Sweden
seta1.1k wrote:

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

 

ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.4 years ago by seta1.1k
0
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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

ADD COMMENTlink written 3.4 years ago by Devon Ryan88k
0
gravatar for h.mon
3.4 years ago by
h.mon24k
Brazil
h.mon24k wrote:

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.

ADD COMMENTlink written 3.4 years ago by h.mon24k

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

ADD REPLYlink written 3.4 years ago by seta1.1k
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