Hello Srinivas, I am glad to hear that you have used Galaxy, because it is just the tool I would recommend to generate the BED file you describe. The Table Browser can do various kinds of intersections, but it has a limitation in that it will only save the identifier for one of the tables used to perform an intersection (the Table Browser doesn't have a join function). Galaxy extends the functionality of the Table Browser.
At galaxy, if you look on the left-hand side of the page for the "Operate on Genomic Intervals" tools, you will find the "Join the intervals of two queries side-by-side". There is a host of other tools in that menu that should help you get exactly what you need. To fetch the repeat regions to add to your table, you can use the "UCSC Main table browser" tool under "Get Data". If you need more help using the Galaxy tools, their helpdesk address is [email protected]. Good luck with your research. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/12/09 16:14, Srinivas Iyyer wrote: > Dear UCSC Genome Browser staff, > > I have positions of small sequence reads on human genome in BED > format. > > Example (first line of BED file) Chr4 22428658 22428696 108 > > I want to intersect these genomic regions with introns of known > genes. I obtained the intronic regions of all genes on chromosome 4. > > > Example (first 2 lines of intronic regions as in BED format) > > Chr4 22359681 22429441 uc003gqp.2_intron_3_0_chr4_22359682_f 0 + Chr4 > 22429599 22429602 uc003gqp.2_intron_4_0_chr4_22429600_f 0 + > > I used a tool from PSU called galaxy which simply intersects genomic regions from both BED files. The results of the intersection is: > > Chr4 22428658 22428696 108 > > In the intron regions file, I have coordinates of an intron but, do not have which gene that intron belongs to and if that intronic region has repeat regions. > > How can I create a BED file that has intronic regions of chr4 and > gene name and repeat region as coloumn > example: Chr4 22359681 22429441 uc003gqp.2_intron_3_0_chr4_22359682_f > 0 + GeneX REpeat regionxxx > > > How can this be done. I appreciate your help. > > > Thank you. > s > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
