Hello everyone!!

My group sequenced multiple hotspots of a panel of genes. Now they want me to create a list with what it is sequenced, with the gene name, the exon and the codon number. I have reached the point to know which are the exonic parts of the bed file, but I am having struggle to associate this data to the main isoform of the gene and the exon and codon number. I am using UCSC Browser, but maybe other software works better. Can you please help me?

Hello,

If you could post a snippet of your input bed file and a line or two of what you hope your output to be, we could provide more details on how to complete this task.

Using the Genome Browser, you could upload the bed file of your hotspot coordinates as a custom track (http://genome.ucsc.edu/cgi-bin/hgCustom). You could then run an intersection on the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) with a genes track of your choice to identify the gene, exon, etc. and pull the data out.

For example, if you want a single representative isoform you could use RefSeq Select and Main, which are NCBI/EBI single transcript choices. For hg19 you could use RefSeq Select.

Feel free to email our public help desk at genome@soe.ucsc.edu. Or you may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.