Oryza Sativa Transcriptome

Question

[EVR]

Hi,

I am new to Plant NGS. COuld anyone suggest me where to find Oryza sativa transcriptome. It would be really great if someone can guide me. Thanks in advance

[GenoMax]

Are you looking to get a GTF file or actual sequence of the transcriptome? iGenomes has the japonica bundle available.

[EVR]

@genomax2 I am looking for Transcriptome with the sequences where I could map the reads and later for down stream analysis

[GenoMax]

You could get the igenomes bundle and then use the information in the GTF file to create a BED file that you can use to get the transcriptome sequence from the full genome.

That said, many choose to align to the genome and then quantify using an appropriate GTF file. You should consider going that route instead of trying to align to transcriptome only.

Answer 1

[Denise CS]

Ensembl Plants seems to have got RNASeq data for leaf, root and panicle tissues mapped (with TopHat) against the reference genome, which can be viewed in the browser.

[GenoMax]

@Denise: @Tom is asking for sequence of rice transcriptome, which I suppose could also be downloaded using BioMart. @Tom: Note this additional option.