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Old 01-10-2014, 03:01 PM   #1
cmccabe
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Default cDNA to genomic position

Is there a tool or script that will convert cDNA cordinates to genomic positions?


c.2T>C to chr15:38545390
c.7G>T to chr15: 38545393
c.7_20del to chr15:38545393
c.26A>T to chr15:38545412
c.30C>A to chr:38545416
c.42T>C to chr15:38591583

Thank you.
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Old 01-13-2014, 05:09 AM   #2
TiborNagy
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I have never heared a tool like that. You need to align cDNA to the genome.
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Old 01-13-2014, 05:48 AM   #3
cmccabe
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Default cDNA to genomic position

The hg19 reference was used for alingnment. Thanks.
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Old 01-13-2014, 05:56 AM   #4
dpryan
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It turns out that those sorts of coordinates are a bit ambiguous (I've reported those sorts of coordinates myself in the past, so I too am guilty here). They only really make sense if a gene has only one splice form. Otherwise, you end up needing to first know which form the coordinates are for. If you know that, then it wouldn't be very tough to put together a little algorithm in R using GenomicRanges and an annotation file.
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Old 01-13-2014, 06:35 AM   #5
tobias.mann
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Default Mutalyzer works pretty well

But it's not scriptable.

https://mutalyzer.nl/positionConverter
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Old 01-13-2014, 06:41 AM   #6
cmccabe
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Default cDNA to genomic position

So the NM_ transcript that was used and coordinate is needed? Thanks.
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Old 01-13-2014, 06:45 AM   #7
dpryan
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Yeah, otherwise you wouldn't know what transcript to use (the example is of SDHD, which has 4 splice forms).
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Old 01-13-2014, 07:05 AM   #8
cmccabe
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Default cDNA to genomic position

So if NM_002880.3 if the transcript for RAF1, what coordinate information is needed? Thank you very much.
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Old 01-13-2014, 07:12 AM   #9
dpryan
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For SNPs, you would just need the position (e.g., the 2 in c.2T>C). For deletions or insertion, you would need the start and width/length. That combined with a transcript designator is enough to reconstruct the genomic coordinates.
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