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Reference genome of wheat for Bowtie

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

genome next-gen assembly sequencing
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updated by JC JC • written by K S • K S

Thank you for your reply and for correcting my question.

I will check at IWGSC pages for more info.

K

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written by K S • K S

Dear Bastien,

Thank you for your reply and for correcting my question.

I will check at IWGSC pages for more info.

K

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written by K S • K S

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

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written by WouterDeCoster WouterDeCoster

Is sRNA referring to smallRNA?

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written by GenoMax GenoMax

Yes indeed, sRNA stands for small RNA

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written by K S • K S

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.

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written by GenoMax GenoMax

1 answer

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

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written by JC JC

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