Hello Lei, One of our scientists reminded me that the intersection function behaves a specific way with gene prediction tables (those with defined exons/blocks). It always performs the intersection based on the alignment exons/blocks, always ignoring any gaps.
To intersect with the entire gene's genomic footprint, the following is suggested. 1. Using table browser, select assembly and gene prediction track of interest 2. For output format, pick "selected fields from primary and related tables" 3. Check all fields except for the last three. This will eliminate the exon/block information. 4. Name the output file and save locally. 5. Re-load the output file as a custom track. 6. Starting with this new modified "gene" custom track, perform an intersection query using your original data, using your original method. Any additional genes that you are able to capture would imply that the peaks in your data fall into intronic regions. This should help to characterize the failures where the gene is mapped to genomic and you manually confirmed coordinate overlap in the assembly browser, but had failed intersection results using the TB. The other issues I mentioned previously (genes unmapped to genomic, or mapped to new genomic location, or removed from data sources) may still apply to some of your data. If you need help determining what happened for these cases, please send data as requested in my previous email. Hope this helps! Jennifer Jackson UCSC Genome Bioinformatics Group Lei Ying wrote: > Hi, there: > This is Lei. I have problem with "intersection" function in "table > browser". > We have a custom track containing genome wide ChIP-Chip peak data in BED > format (mm8) and we try to find out which genes those peaks intersect. > Then we intersect our custom track with Knowgene table on Knowgene track > (mm8) and we found some genes with peaks are missing in the gene list. > The next thing we did is to liftover our BED format to mm9, and redo the > intersection. These genes still cannot be recognized after intersection. > We also tried to intersect our custom track with RefSeq table, and had > the same problem. > Do we miss some tricks during the procesee? If you could provide us a > detailed manual of how to use table browser, it will be a great help. > UCSC genome browser is something I cannot live without. THX for your > work. It's really cool. > Look forward to your reply. > Sincerely, > > > Lei Ying, MD, Ph.D > Postdoctoral Fellow > Department of Hematology > The Children's Hospital of Philadelphia > Philadelphia, PA, 19104 > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
