[laura]

I am again not an expert in GRC patches but looking at

http://www.ncbi.nlm.nih.gov/projects...ta/index.shtml for GRCh37.p7 would make me think that 60 fix patches have been aligned to scaffolds from the primary assembly

[shyam_la]

Well, I thought you could interpret it for me.. What has changed 60 transcripts? 60 base pairs? 60 what? Sorry I have no idea what "60 fix patches have been aligned to scaffolds from the primary assembly " really means..

[shyam_la]

Biotype "non-coding transcript" is also included for sure, as they have been annotated as such when I used refseq genes..

The Refseq cdna set will probably only considers protein coding transcripts/cdnas

Ensembl's 57000 includes not just protein coding genes but also pseudogenes, ncRNAs and some other things

If you go to biomart and just look at protein coding genes you get 21976 genes

[laura]

Well, I thought you could interpret it for me.. What has changed 60 transcripts? 60 base pairs? 60 what? Sorry I have no idea what "60 fix patches have been aligned to scaffolds from the primary assembly " really means..

Oddly enough the GRC help does explain these things

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/patches.shtml

[shyam_la]

Thank you so much Laura!

[bwubb]

Hello,

Does anyone know of a reference file or anything that lists the primary transcript IDs along with their matching official gene symbol? I would love both NM and ENS ids, but I would take either. Every file I have found so far will list every single transcript ID and since their isn't any exact ordering within the various IDs for genes I have to check using ENSEMBL/NCBI.

Im finding it tedious to identify every single one manually since I am working with exome data.

Thank you.

[bwubb]

The more I think about this, the more I realize it just isnt possible...

Oh well.

[laura]

You can do this with biomart

Look at this canned query

http://www.ensembl.org/biomart/martv...L=resultspanel

and the biomart tutorials

http://www.youtube.com/watch?v=DXPaBdPM2vs