cDNA to genomic position

cmccabe · 01-10-2014, 03:01 PM

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.

TiborNagy · 01-13-2014, 05:09 AM

I have never heared a tool like that. You need to align cDNA to the genome.

cmccabe · 01-13-2014, 05:48 AM

The hg19 reference was used for alingnment. Thanks.

dpryan · 01-13-2014, 05:56 AM

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.

tobias.mann · 01-13-2014, 06:35 AM

But it's not scriptable.

https://mutalyzer.nl/positionConverter

cmccabe · 01-13-2014, 06:41 AM

So the NM_ transcript that was used and coordinate is needed? Thanks.

dpryan · 01-13-2014, 06:45 AM

Yeah, otherwise you wouldn't know what transcript to use (the example is of SDHD, which has 4 splice forms).

cmccabe · 01-13-2014, 07:05 AM

So if NM_002880.3 if the transcript for RAF1, what coordinate information is needed? Thank you very much.

dpryan · 01-13-2014, 07:12 AM

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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01-10-2014, 03:01 PM	#1
cmccabe Senior Member Location: chicago Join Date: Jul 2012 Posts: 354	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.

01-13-2014, 05:48 AM	#3
cmccabe Senior Member Location: chicago Join Date: Jul 2012 Posts: 354	cDNA to genomic position The hg19 reference was used for alingnment. Thanks.

01-13-2014, 06:35 AM	#5
tobias.mann Junior Member Location: Ann Arbor, MI Join Date: Feb 2013 Posts: 2	Mutalyzer works pretty well But it's not scriptable. https://mutalyzer.nl/positionConverter

01-13-2014, 06:41 AM	#6
cmccabe Senior Member Location: chicago Join Date: Jul 2012 Posts: 354	cDNA to genomic position So the NM_ transcript that was used and coordinate is needed? Thanks.

01-13-2014, 05:09 AM	#2
TiborNagy Senior Member Location: Budapest Join Date: Mar 2010 Posts: 329	I have never heared a tool like that. You need to align cDNA to the genome.

01-13-2014, 05:56 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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.

01-13-2014, 06:45 AM	#7
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Yeah, otherwise you wouldn't know what transcript to use (the example is of SDHD, which has 4 splice forms).

01-13-2014, 07:05 AM	#8
cmccabe Senior Member Location: chicago Join Date: Jul 2012 Posts: 354	cDNA to genomic position So if NM_002880.3 if the transcript for RAF1, what coordinate information is needed? Thank you very much.

01-13-2014, 07:12 AM	#9
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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.