Question: Arabidopsis indexed genome
0
gravatar for schlogl
9 months ago by
schlogl70
Brazil-Florianopolis
schlogl70 wrote:

Hey guys do you know where I can find the indexed genome for Arabidopsis thaliana for using with hitsat2? Thanks for any direction.

I think I found it.

Paulo

next-gen • 269 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by schlogl70
1

I got it. ftp://ftp.ensemblgenomes.org/pub/plants/release-45/fasta/arabidopsis_halleri/dna_index/ Thanks

ADD REPLYlink written 9 months ago by schlogl70
1

This index is not something you can use with hisat2. You will need to build your own starting with the fasta genome sequence.

ADD REPLYlink written 9 months ago by genomax90k
1

This is also the halleri, not thaliana genome, be aware. I will untoggle the accepted status to avoid confusion.

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint39k

Thanks I was trying to avoid that but...8(

ADD REPLYlink written 9 months ago by schlogl70
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