converting between genome and transcripts coordinates

[leshkowitz]

I need to calculate the exon distance from regions in UTR to the CDS start and I have mm10 genomics coordinates (bed file). I prefer to use refSeq transcripts.

Any pointers would be greatly appreciated.

[neavemj]

What does the bed file look like? Maybe a combination of grep and awk could work?

[leshkowitz]

My bed file has six columns-

chr10 115315572 115315581 Rab21 9 -
chr10 115362113 115362122 Tmem19 9 -
chr10 115362167 115362176 Tmem19 9 -

Thanks

[neavemj]

Hi leshkowitz,

What annotation is being shown in your bed file? Seems to be very small regions, followed by a gene symbol. Does this file contain all the information that will be needed to calculate 'exon distance' - i.e., UTR and CDS start positions?

Matt.