Question: Where can I download the Danio Rerio (zebrafish) transcriptome?
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gravatar for dtatarak
11 months ago by
dtatarak10
dtatarak10 wrote:

I've been working with several RNA-seq data sets in zebrafish, and I largely use STAR for my alignments. For that, I have a full genome fasta file and a gtf. Simple enough. however, I would like to try using SALMON, and it requires a transcriptome file to build its index. I found what I thought was a zebrafish transcriptome file from UCSC, however, SALMON is running into errors building an index with it. It seems to think what I've given it is actually a genome not a transcriptome. I've looked on Ensembl, and I cannoth find a transcriptome file at all.

Does anyone know where I can find a transcriptome file for Zebrafish? Thanks!

ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 11 months ago by dtatarak10
2

SALMON is running into errors building an index with it. It seems to think what I've given it is actually a genome

What are the errors?

ADD REPLYlink written 11 months ago by h.mon30k
4
gravatar for Jean-Karim Heriche
11 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

I don't know what kind of transcriptome file you want but Ensembl certainly has a FASTA file with all transcripts (transcripts file have cDNA in the name). If that's not what you want, you can also use the perl API to extract the exact data you need and put it in the format you want.

ADD COMMENTlink written 11 months ago by Jean-Karim Heriche22k
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