Question: Download ONLY primary transcripts from plants
0
gravatar for aboutmb
18 months ago by
aboutmb0
Brazil
aboutmb0 wrote:

Hi, everyone!

I study flowering plants and I need to download only primary transcripts from them. So I've been using Phytozome for this purpose. But I'ld like to work with as many as possible species and Phytozome has restricted number of species.

So, does anyone know anyway to obtain accurate primary transcripts besides Phytozome?

Thank you so much!

ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 18 months ago by aboutmb0
1

PLAZA

comprehensive list of species but not exhaustive either

ADD REPLYlink written 18 months ago by lieven.sterck8.7k

Check Ensembl plants.

ADD REPLYlink written 18 months ago by genomax91k

I've checked, but Ensembl hasn't only primary transcripts. I've compared Ensembl and Phytozome for some species and I got different number of sequences.

Thank you anyway!

ADD REPLYlink written 18 months ago by aboutmb0
3

No site is likely to list primary transcripts alone since that is a concept subject to change/interpretation. What is your criteria for calling something a primary transcript? That it be the longest and/or most abundant?

Number of isoforms you are going to see is going to be different for each site based on their method of annotation/evidence being used for that annotation.

ADD REPLYlink written 18 months ago by genomax91k
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