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Old 03-28-2018, 05:35 AM   #1
leshkowitz
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Default converting between genome and transcripts coordinates

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.
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Old 03-28-2018, 03:29 PM   #2
neavemj
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What does the bed file look like? Maybe a combination of grep and awk could work?
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Old 03-28-2018, 10:37 PM   #3
leshkowitz
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My bed file has six columns-

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

Thanks
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Old 04-02-2018, 05:55 PM   #4
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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.
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cds, distance, genome coordinates, transcripts, utr

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