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
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worarado.kan •
1 answer
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
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