Fetching transcripts from rna seq sra dataset

[cakeinspace]

Hello thanks for the wonderful work. I am interested in downloading all transcripts for a given gene from the rna seq datasets available in sra.

Is there a way to specify the metadata such as species name etc and the gene of interest and fetch the transcripts along with the associated metadata.

From reading the tutorials. One way i could figure out was to simply get all accession ids for rna seq in sra and then provide the gene of interest as a fasta and run the tutorial as in chicken.md.

I just wanted to know if theres a smarter way or am i completely off

Thanks in advance

[rchikhi]

Hi,

your best bet is to familiarize yourself with https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud-based-examples/ to grab a list of datasets which are for sure rna-seqs from the species that interests you.

If you need assistance with this, please post here.

best, Rayan

[rchikhi]

Ah, to answer your question, there is currently no way to specify gene of interest, we didn't annotate the Logan assembled sequences/transcripts one by one nor did we call genes on them (yet)