Hi Adriana, The 4th column of a BED file is the score column: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED and in this instance, is given the default value of "0".
The one-off difference between BED and the GTF output has to do with the way that these formats are defined. For BED, the first base in a chromosome is numbered as 0: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED, however for GTF the first base in a chromosome is numbered as 1: http://genome.ucsc.edu/goldenPath/help/customTrack.html#GTF http://mblab.wustl.edu/GTF2.html. I hope this information is helpful. Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 6/14/11 4:30 PM, Pitea Adriana wrote: > Hi everyone. > What I'm trying to find out is the meaning of the 4th column of the file I > obtain when I select in Table Browser: genome assembly hg19, RefSeq Genes -> > Exons. Am i doing this right?What I want is to obtain the coordinates of the > exons in the human genes and compare them to another set of coordinates and > see how many overlap. The thing is I don't really understand what I see on > the 4th coloumn: For example I have this set of exons:chr1 8384389 > 8384786 NM_001080397_exon_0_0_chr1_8384390_f 0 + > chr1 8385357 8385450 NM_001080397_exon_1_0_chr1_8385358_f 0 + > chr1 8385877 8386102 NM_001080397_exon_2_0_chr1_8385878_f 0 + > chr1 8390268 8390996 NM_001080397_exon_3_0_chr1_8390269_f 0 + > chr1 8395496 8395650 NM_001080397_exon_4_0_chr1_8395497_f 0 + > chr1 8397875 8398052 NM_001080397_exon_5_0_chr1_8397876_f 0 + > chr1 8399552 8399758 NM_001080397_exon_6_0_chr1_8399553_f 0 + > chr1 8403806 8404227 NM_001080397_exon_7_0_chr1_8403807_f 0 + > Am i given the coordinates for each exons on a certain gene? And if so why is > it that when I look at the coordinates of the gene that corresponds to the id > NM_001080397 it starts later than the exon??:chr1 hg19_refGene CDS > 8384390 8384786 0.000000 + 0 gene_id "NM_001080397"; > transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8384390 8384786 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8385358 8385450 0.000000 + 2 > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8385358 8385450 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8385878 8386102 0.000000 + 2 > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8385878 8386102 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8390269 8390996 0.000000 + 2 > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8390269 8390996 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8395497 8395650 0.000000 + 0 > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8395497 8395650 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8397876 8398052 0.000000 + 2 > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8397876 8398052 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8399553 8399758 0.000000 + 2 > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene exon 8399553 8399758 0.000000 + . > gene_id "NM_001080397"; transcript_id "NM_001080397"; > chr1 hg19_refGene CDS 8403807 8404070 0.000000 + 0 > gene_id "NM_001080397"; transcript_id "NM_001080397";Thank you,Best,Adriana > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
