Mate pair distance calculation

BioKiwi · 09-29-2014, 11:27 PM

Hi

I have two mate pair libraries with 2-3 kb and 6-8 kb inserts from a plant species. The libraries have been sequenced 2x100 cycles. FastQC shows good quality reads with low duplication levels. I do not have a reference genome for the species. I wondering if there is an easy way to check the distance between paired reads to see how many of reads are from the expected fragments sizes.

pmiguel · 09-30-2014, 09:51 AM

No. It is not possible without a reference.
You could do an assembly to generate a reference. abyss-PE calculates the pair distances during assembly.

--
Phillip

BioKiwi · 09-30-2014, 01:06 PM

Thanks pmiguel. Is mapping to organnells genome is a good option. I know that their size is smaller in comparison to nuclear genome, but they are available for some close relatives of the species.

GenoMax · 09-30-2014, 02:44 PM

You could try that. Depending on how close your sample genome is to the one you are using as a reference you will get an answer. That may not necessarily be accurate but would at least give you a ball park idea of the insert size distribution.

pmiguel · 10-01-2014, 04:55 AM

Quote:

Originally Posted by BioKiwi

Thanks pmiguel. Is mapping to organnells genome is a good option. I know that their size is smaller in comparison to nuclear genome, but they are available for some close relatives of the species.

Yes. Also, for plant samples you can usually assemble the chloroplast from just a fraction of the data because of the high molar contribution of chloroplast DNA to most plant genomic DNA preps.

But mapping to a relative would likely work as well. Doesn't matter if there areas that don't map, these areas have no reason to create bias in inter-pair distance measurements.

--
Phillip

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09-29-2014, 11:27 PM	#1
BioKiwi Member Location: KiwiTeritory Join Date: Sep 2014 Posts: 19	Mate pair distance calculation Hi I have two mate pair libraries with 2-3 kb and 6-8 kb inserts from a plant species. The libraries have been sequenced 2x100 cycles. FastQC shows good quality reads with low duplication levels. I do not have a reference genome for the species. I wondering if there is an easy way to check the distance between paired reads to see how many of reads are from the expected fragments sizes.

09-30-2014, 09:51 AM	#2
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	No. It is not possible without a reference. You could do an assembly to generate a reference. abyss-PE calculates the pair distances during assembly. -- Phillip Last edited by pmiguel; 10-01-2014 at 04:55 AM.

09-30-2014, 01:06 PM	#3
BioKiwi Member Location: KiwiTeritory Join Date: Sep 2014 Posts: 19	Thanks pmiguel. Is mapping to organnells genome is a good option. I know that their size is smaller in comparison to nuclear genome, but they are available for some close relatives of the species.

09-30-2014, 02:44 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	You could try that. Depending on how close your sample genome is to the one you are using as a reference you will get an answer. That may not necessarily be accurate but would at least give you a ball park idea of the insert size distribution.