Question: Mapping scaffolds to another reference genome
1
gravatar for ash.t.cook
3.3 years ago by
ash.t.cook10
Oxford
ash.t.cook10 wrote:

Hello,

I have mapped RAD-PE reads to a reference genome (that consists only of scaffolds without the assignment of scaffolds to any chromosome) and called SNPs. However, in order to answer my research question I now need to align reads (that are now mapped to reference genome scaffolds) to the Zebra Finch genome (as this is the closest complete genome to my study species).

My question is that what the best software (and method) to do this?

Thank you very much for your help in advance

p.s. I am relatively new to bioinformatics!

snp alignment genome • 2.7k views
ADD COMMENTlink modified 3.3 years ago by Joseph Hughes2.8k • written 3.3 years ago by ash.t.cook10
3
gravatar for Joseph Hughes
3.3 years ago by
Joseph Hughes2.8k
Scotland, UK
Joseph Hughes2.8k wrote:

Don't map the reads back to the Zebra Finch genome. Use your scaffolds sequences with the Zebra finch genome to combine them using a tool like Mummer, scaffold_builder. There are many more tools, you need to look for "scaffolding a genome to a reference genome".

ADD COMMENTlink written 3.3 years ago by Joseph Hughes2.8k

Fantastic thank you so much!

ADD REPLYlink written 3.3 years ago by ash.t.cook10
0
gravatar for vmicrobio
3.3 years ago by
vmicrobio250
vmicrobio250 wrote:

you can use bowtie2 to align reads to your reference genome

ADD COMMENTlink written 3.3 years ago by vmicrobio250
bowtie2 -p 8 -x ZebraFish-genome data.fastq > alignment.sam

with -p as cpu (8) and -x the genome index prefix (ZebraFish-genome)

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by vmicrobio250
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