cDNA sequences

[Jane Bugler]

To whom it may concern ,

I am inquiring about how best to visualise and get the sequence of cDNA on the USCS genome browser. If there are any tutorials, they would also be most appreciated.
Kindest regards,

Jane

------------------------
Ms Jane Bugler
PhD Candidate
Institute of Cancer Sciences
Wolfson Wohl Cancer Research Centre
University of Glasgow
Garscube Estate
Switchback Road
Glasgow, G61 1QH

[Matthew Speir]

Hi Jane,

Thank you for your question about visualizing and obtaining sequence for
cDNAs in the UCSC Genome Browser.

Some tracks in the UCSC Genome Browser contain cDNA sequences, such as
the "mRNAs" tracks. For example, here is the description page for the
"Human mRNAs" track on the hg38/GRCh38 assembly of the human genome:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=mrna. Here you can
see this mRNAs track in the Genome Browser alongside the GENCODE v22
track for the SOD1 gene:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeir&hgS_otherUserSessionName=hg38_Sod1mRnaMlq

We just released a YouTube video that details how to obtain the sequence
for items in the track of your choice:
http://genome.ucsc.edu/training/vids/index.html#vid08. I would start at
time "5:40" in the video, which is where the steps describing how to get
sequence begin. While the video describes getting the sequence for items
in a different track, you can adapt the steps to your needs by selecting
"group: mRNA and EST", "track: Human mRNAs", and "table: all_mrna".

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group