Question: Reference genome of wheat for Bowtie
0
gravatar for K S
5 weeks 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 5 weeks ago by JC7.6k • written 5 weeks 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 5 weeks ago • written 5 weeks ago by Bastien HervĂ©3.7k

Thank you for your reply and for correcting my question.

I will check at IWGSC pages for more info.

K

ADD REPLYlink written 5 weeks ago by K S0

Is sRNA referring to smallRNA?

ADD REPLYlink written 5 weeks ago by genomax63k

Yes indeed, sRNA stands for small RNA

ADD REPLYlink written 5 weeks 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 5 weeks ago • written 5 weeks ago by genomax63k
3
gravatar for JC
5 weeks ago by
JC7.6k
Mexico
JC7.6k 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 5 weeks ago by JC7.6k
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