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Old 09-20-2016, 08:25 AM   #1
hyacinth2011
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Location: United States

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Default Where to get reference fasta transcriptome for Salmon?

Hello -

My apologies to everyone on the forum. I am a new user of NGS tools. My question is very basic:

For running Salmon where do I find the reference transcriptome for zebrafish GRCz10? Is this the same as the genome fasta file on iGenomes (http://support.illumina.com/sequenci...igenome.html)?

Many thanks!
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Old 09-20-2016, 09:49 AM   #2
SamCurt
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No, that's the genomic sequence. For these you'd need to check the major genome databases; I guess you mean these:
  1. NCBI: ftp://ftp.ncbi.nih.gov/refseq/D_reri...h.1.rna.fna.gz
  2. UCSC: http://hgdownload.soe.ucsc.edu/golde...ips/mrna.fa.gz or http://hgdownload.soe.ucsc.edu/golde.../refMrna.fa.gz
  3. Ensembl: The list is here: http://useast.ensembl.org/info/data/ftp/index.html; choose the link you need.
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