Reference genome of wheat for Bowtie

Question

[K S]

Hi,

I would like to align my sRNA reads from .FASTQ file to the wheat reference genome. However, I am not sure which site to use for obtaining the reference genome?

Do I need the .FASTA or .GBFF file?

Is this correct?

bowtie -q -v 0 -k 10 -S -t  (wheat-ref.index) (input.fastaq)

Thank you

[Bastien Hervé]

Hello K S,

This is a question not a tool, Tool section is used to highlight a new software.

Could you please correct some misspelling like :

reads from fastaq file

fasta or fastq ?

.fast

fasta or fastq ?

Take a look here for reference genome and annotation : http://www.wheatgenome.org/Projects/IWGSC-Bread-Wheat-Projects/Reference-genome

[K S]

Thank you for your reply and for correcting my question.

I will check at IWGSC pages for more info.

K

[GenoMax]

Is sRNA referring to smallRNA?

[K S]

Yes indeed, sRNA stands for small RNA

[GenoMax]

Would it not be better to get RNA's from Wheat from RNAcentral here and align against those? Look in left column to see what kind of RNA's you would want.

Answer 1

[JC]

I generally use Phytozome or Ensembl Plants for plant genomes. You need the FASTA file to create your index with bowtie-build command.