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Recommendation needed: mRNA download

Hey all, I would like to obtain or download mRNA data for an organism ( Amphioxus) is there a database where I can get it? ncbi was suggested but I couldn't navigate to it. can someone guide me or share a link please? I tried one guide on here and wasn't successful. Thanks

gene rna-seq refseq mrna
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updated by GenoMax GenoMax • written by jaqx008 jaqx008

NCBI sounds like a good way to go, why could you not navigate throught it ? What was your guide and why it was not successful ?

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written by Bastien Hervé Bastien Hervé

The link RefSeq and mRNA was a guid to obtaining the human mRNA. I went to ncbi and was only able to see information/tutorial on Homo sapien

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written by jaqx008 jaqx008

2 answers

Presumably they meant SRA, which is where most sequencing data is stored.

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written by Devon Ryan Devon Ryan

I think the sequence read achive are just set of RNA seq data and not mRNA data.

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written by jaqx008 jaqx008

If you want a reference transcriptome then see the link from Genomax. Most of us would interpret "mRNA data" as mRNA-seq data.

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written by Devon Ryan Devon Ryan

You can search NCBI nucleotide/RefSeq database using the following terms: Amphioxus AND srcdb_refseq[PROP]. There are 28K entries at this time.

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written by GenoMax GenoMax

So I somehow managed to play around different databases since the ncbi was still confusing and finally found the floridae database were I downloaded the fa file. but the fasta headers look like this >112690 >257564 etc. I want to convert this to a bed file. but the loci names in my original genome file doesnt match this new fa file. I can do 1. fasta to bam then bam to bed ( but this still has the headers i dont desire) 2. map the fasta to the genome and get an aligned fasta then repeat step 1 above, but I still get the undesired headers in the new fasta and bed. Any suggestions please?

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written by jaqx008 jaqx008

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