Hi Ahmed, Our mailing list strips attachments, so I wasn't able to see your attachment. However, I repeated your steps so I knew what your data looked like.
The BED format link you mentioned, http://genome.ucsc.edu/FAQ/FAQformat.html#format, describes 12 columns, which are the same 12 columns that I see in the output I got after following your steps. So, all the columns (1-12) described in the BED information link are the same columns in your output. As you can see from that BED format link, the +/- column (the 6th column) is the column indicating which strand the gene is on: 6. strand - Defines the strand - either '+' or '-'. So, this is not the column to rely on. However, if you followed the steps you provided, all the genes listed in your output contain CpG islands because of the intersection that you did. I hope this information is helpful. Please contact the mail list ([email protected]) again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group On 7/28/11 8:21 PM, Ahmed H Khamas wrote: > Dear respected, > > First please accept my apology for disturbing you with my email, I'm writing > to you to have some explanation about how to interpret the genes list table > result so that I can decide whether the gene has a CpG island or not! I > could not understand it through the help option in Table browser! > > Actually I did all what you have mentioned in a post in Bioforum and got the > data (Attached the 1st 20 genes from 3000 in Excel file), but I did not know > how to interpret the data and whether the column with +/- is the one that I > should rely on!? > > I could only put the labels of 8 columns to BED data from this link > (http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ) after that I don't know > what the rest of columns mean. > > > > To make the custom track, I did the following: > > clade: mammal, genome: Human, assembly: Feb. 2009 > > group: Regulation, track: CpG Islands > > table: cpgIslandExt, region: genome > > output format: Custom Track > > click: "Get output" > > click: "Get custom track in table browser" > > > > and in Table browser; > > clade: mammal, genome: Human, assembly: Feb. 2009 > > group: Genes and Gene Prediction Tracks, track: RefSeq Genes > > table: refGene > > region: genome > > Identifiers: (paste in the names of the genes) > > Intersection: On the intersection menu page, change to: > > group: Custom Tracks > > track: CpG Islands Custom Track (the default name was bt-cpgIslandExt) > > table: CpGIslandExt (bt_cpgIslandExt) or whatever you named it. > > press submit > > output format: BED > > click: "get output" then get out put in a file format > > > > Thank you in advance for your kind help, > > > > Best regards, > > > Ahmed Khamas > > > M.B.Ch.B, PhD candidate > > Surgical Oncology Department > > Medical Faculty, Tokyo Medical and Dental University > > > > _______________________________________________ > Genome-mirror mailing list > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
