Mapping scaffolds to another reference genome

Question

[ash.t.cook]

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!

Answer 1

[Joseph Hughes]

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".

[ash.t.cook]

Fantastic thank you so much!

Answer 2

[vmicrobio]

you can use bowtie2 to align reads to your reference genome

[vmicrobio]

bowtie2 -p 8 -x ZebraFish-genome data.fastq > alignment.sam

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