Question: Arabidopsis indexed genome
0
gravatar for schlogl
5 days ago by
schlogl50
schlogl50 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 • 67 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by schlogl50
1

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

ADD REPLYlink written 5 days ago by schlogl50
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 5 days ago by genomax75k
1

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

ADD REPLYlink modified 5 days ago • written 5 days ago by ATpoint26k

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

ADD REPLYlink written 5 days ago by schlogl50
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