How to build index of reference scaffold.fasta using bowtie?

Question

[worarado.kan]

Hello everyone, I'm new for running bioinformatics. Now I have the blueberry genome from this site: http://www.igbquickload.org/blueberry/V_corymbosum_scaffold_May_2013/ file called: V_corymbosum_scaffold_May_2013.fa.gz and in this file showed like this After that I would like to map with my read data using Bowtie program. Should I build index of my reference before aligning with bowtie? What is the command for do that? or What should I do, please recommend me?

Thank you so much everyone Kan

Answer 1

[Bastien Hervé]

Yes, you have to build your index before alignment

See here how to build an index with bowtie2 : http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer

Should be something like this :

bowtie2-build V_corymbosum_scaffold_May_2013.fa.gz blueberry_index