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Reference genome of wheat for Bowtie
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15 months ago
K S • 0

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

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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

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Thank you for your reply and for correcting my question.

I will check at IWGSC pages for more info.

K

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Is sRNA referring to smallRNA?

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Yes indeed, sRNA stands for small RNA

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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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11 months ago
JC 7.9k
Mexico

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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