Question: Creating a Bowtie2 Index for S.Purpuratus to use in Galaxy
0
gravatar for alice_pieplow
14 months ago by
alice_pieplow0 wrote:

I want to align some WGS data I have for S. purpruatus (purple urchin) using bowtie2 in Galaxy, but the reference genome for the organism is not available. I have the option to upload my own reference index- how do I make one? I believe this is the most current reference genome; where do i start? ftp://ftp.ncbi.nih.gov/genomes/Strongylocentrotus_purpuratus/

I am honestly so new to this- I dont even know which of these file directories contains the actual genome, it looks like a lot of them are transcripts or annotations. Any help is greatly appreciated!

ADD COMMENTlink modified 14 months ago by genomax68k • written 14 months ago by alice_pieplow0
2
gravatar for genomax
14 months ago by
genomax68k
United States
genomax68k wrote:

Download the genome in fasta format from here. Upload to galaxy and then create bowtie2 index.

ADD COMMENTlink modified 14 months ago • written 14 months ago by genomax68k

Just adding to what genomax wrote: Upload the FASTA file of the genome into your history and then you will be able to choose "Use a genome from the history and build index" when asked about the reference during the alignment step.

ADD REPLYlink written 14 months ago by Friederike4.4k

It worked perfectly! Thanks so much :)

ADD REPLYlink written 13 months ago by alice_pieplow0
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