How to build a transcriptome reference ?

Question

[vin.darb]

Hi !

I work with Arabidopsis thaliana RNA-Seq data, and I would like to test Salmon for some downstream transcripts quantification analysis.

In order to compare results with a publication, I work with TAIR10 references files.

Salmon require a transcriptome reference in .fasta format, unfortunetly, there is no transcriptome available with TAIR10. I have the genome reference (.fasta of the 5 chromosomes), and the GTF file for genes annotation.

With these 2 files, is it possible to produce a reference transcript?

All the best

Answer 1

[AK]

Perhaps TAIR10_cds_20110103_representative_gene_model_updated and TAIR10_cdna_20110103_representative_gene_model_updated? Or gffread.

[vin.darb]

Oh thank’s, I didn’t see that ... :x

edit:

the last update is here: https://www.arabidopsis.org/download_files/Sequences/TAIR10_blastsets/TAIR10_cdna_20101214_updated