Question: Reference genome of wheat for Bowtie
0
gravatar for K S
8 months ago by
K S0
K S0 wrote:

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

ADD COMMENTlink modified 8 months ago by JC8.7k • written 8 months ago by K S0
1

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

ADD REPLYlink modified 8 months ago • written 8 months ago by Bastien HervĂ©4.4k

Thank you for your reply and for correcting my question.

I will check at IWGSC pages for more info.

K

ADD REPLYlink written 8 months ago by K S0

Is sRNA referring to smallRNA?

ADD REPLYlink written 8 months ago by genomax73k

Yes indeed, sRNA stands for small RNA

ADD REPLYlink written 8 months ago by K S0

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.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax73k
3
gravatar for JC
8 months ago by
JC8.7k
Mexico
JC8.7k wrote:

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

ADD COMMENTlink written 8 months ago by JC8.7k
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