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Where can I download the Danio Rerio (zebrafish) transcriptome?

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!

zebrafish transcriptome rna-seq genomics salmon
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updated by Biostar Biostar • written by dtatarak • dtatarak

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?

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written by h.mon h.mon

1 answer

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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