Previously annotated gene symbols

[Rachael Kuintzle]

Hello,

I am trying to find an annotation file that lists MiTranscriptome gene IDs along with current gene symbols, for genes that correspond to previously known genes. I think I'm just not looking in the right place! Does such a file exist?

Thank you,

Rachael

[Dan E. Webster]

I would also love to see a file with this information to complement the GTF file.  Do you have the attribute files after the Cuffmerge call, which would contain a mapping of transcript_id or gene_id back to Gencode ID?

Thanks for the great resource!

All my best,

Dan

Dan E. Webster

Damon Runyon Postdoctoral Fellow

Laboratory of Louis Staudt

NCI/NIH

[Yashar Niknafs]

Hello, 

Will send you this file shortly! Sorry for the delay. 

-Yashar

[Yashar Niknafs]

[samha...@gmail.com]

Hello Yashar,

Would it be possible to email me with the information described in this thread too, please? Also, do you happen to have the actual sequences of the lncRNAs discovered, or do you just have the coordinates?

Many thanks and best wishes,

Sam

[Yashar Niknafs]

Hi Sam,

Check this out and let me know if it doesn't cover what you need: 

Look here: https://groups.google.com/d/msg/mitranscriptome/hpxMMwo5ysM/L9rg4yVvBQAJ

Regarding sequences: There are some good utilities out there to extract sequence information from a GTF. 

The cufflinks gffread utility can do it without too much trouble: 

http://cole-trapnell-lab.github.io/cufflinks/file_formats/#the-gffread-utility

Let me know if you have trouble getting those sequences.

-Yashar 

[samha...@gmail.com]

Hi Yashar,

Thank you for the advice on extracting the lncRNA sequences. Also, thank you very much for the metadata file, though it is not exactly what I am looking for. Primarily, I am looking to match up MiTranscriptome IDs (either gene or transcript ids) with existing annotations, e.g. Ensembl or Gencode. I am wondering if you have a file which has this information, please?

Many thanks again!

Sam

[jssc...@gmail.com]

Hello,

I am looking for the exact same information as Sam and would be very grateful if you could share it with me as well, please?

Thank you very much for your efforts.

Best,

Jonas

Jonas Schulte-Schrepping

Limes Institute Bonn

Department for Genomics & Immunoregulation

Rheinische Friedrich-Wilhelms-University Bonn

[zhaozux...@gmail.com]

Hello,

I am also looking for the Ensembl IDs or gene symbol for all lncRNAs and coding genes, could you please share that information with me?

Thank you so much.

Best regards,

Xianglan

[daniel Gautheret]

Dear all, 

In line with this thread: can I get the equivalence table between Mitranscriptome gene_id and either ENSG or Gene symbols? 

Thanks!

Daniel