Ucsc Track Friendly Format For Cds Sequences And Coordinates?
I want to represent a set of sequences that occur within CDS regions of genes and then load these as UCSC tracks to browser. I need to fetch the CDS sequence of a gene, see where my sequences of interest lie, and then output that as a format loadable in a track in UCSC. What is the right format for this? It would need to represent spliced alignments since CDS coordinates are different from the genomic coordinates. Is there an easy and flexible format to keep all necessary info in?
• 2,721 views
•
link
updated
by
Devon Ryan
•
written
by
user
•
written
by
user
1 answer
Probably BAM or GTF/GFF would be the most convenient. With BAM, you could put the relevant sequences in and show splicing with CIGAR operators.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
No mouseOver effect in my track hub on UCSC genome browser
written by Pei
-
manually turn off multiple tracks at once in UCSC browser
written by fraser518 •
-
Tool: UCSC Custom Track Generator Script
written by steve
-
Extracting promoter regions alignment
written by prosvirov.k •
-
How to find overlaps between tracks from UCSC in R
written by sebastianzeki0
-
UCSC Table Browser: redundant CDS sequences in generated fasta
written by lilla.davim
-
Adding Custom Bed And Bam Tracks To UCSC Browser By URL
written by user
-
Coverting Gff/Gtf To Bed Or Other Format Displayable By Ucsc Genome Browser?
written by user
-
Defining Region Of Interest Inside A Track In Igv
written by Rossella •
-
Aa Sequence From The Human Proteins Track
written by Klugman •
I don't understand why you cannot use something like bed or bigBed. Both support "introns". Do you know these formats? Or have you eliminated them for some reason? They both well documented and can be used from customTracks or track hubs.