Recommendation needed: mRNA download

Question

[jaqx008]

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

[Bastien Hervé]

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 ?

[jaqx008]

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

Answer 1

[Devon Ryan]

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

[jaqx008]

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

[Devon Ryan]

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

Answer 2

[GenoMax]

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

[jaqx008]

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?