Reference transcriptome ?

Question

[lilla.davim]

Hello,

Is there somewhere a reference (human) transcriptome available for download (e.g. as fasta)?

If yes where can I find it and how is it obtained? The concatenation of the longest transcripts of all genes?

Thanks for your help.

[lilla.davim]

Ok thanks, so I guess to get the transcriptome I need to select:

• group = mRNA and EST
• track = human mRNAs
• table = all_mrna
• region = genome

This however gives me only the mRNAs, and I thought a transcriptome also included other types of RNAs. Is this wrong? If not I did not see how I could get this "more general" transcriptome in the Table Browser. Any clue?

[David Langenberger]

I would go for 'genes and gene predictions' and then e.g. 'gencode'. If you want more, you can add the 'snoRNAs and microRNAs' track, the 'tRNA track', or whatever you want. You can also download all tracks and merge them. Whatever you want/need. As long as it makes sense, the definition of your 'transcriptome' is completely in your hands. Some tracks/databases are more trustworthy than others. Go to the 'manufacturers' page and check what they did and decide if you trust it. Bioinformatics sometimes means a lot of reading, research and testing. Never just trust these data. That's at least my opinion. :)

[lilla.davim]

Hello,

Thanks but in the UCSC Table Browser if I select:

• Table: Groups and group predictions
• Track: GENCODE Genes V19
• Table: Basic (wgEncodeGencodeBasicV19)

Then I where do I specify that I want RNAs (i.e. sequence of the transcriptome)?

[Devon Ryan]

Just set the output format to "sequence", you can then select whether you want CDS, UTR as well, etc.

Answer 1

[David Langenberger]

The UCSC Table Browser will help you.

Answer 2

[Fedor Gusev]

You can download FASTA files from Ensembl: ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cdna/ and ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/ncrna/. But be sure to check if ncRNA set is included into cDNA set -- I am not sure about it.