transcriptome assembly-comparative genomics

bioman1 · 07-30-2012, 09:22 AM

I have three different transcriptome assemblies (Kmer 30,35 & 65) of one insect species. I want to compare transcriptome assemblies with reference insect sequence(from ensembl). I want to know how many genes show up in all kmer assemblies and between individual assemblies (i.e between 30 & 35, between 35 & 65). I would like to get idea to better way to compare to get list of genes. Any journal paper info regarding this will be helpful.

DZhang · 07-30-2012, 06:50 PM

Hi Bioman1,

Can you share the purpose behind your proposed steps? Please look into whether CD-HIT is the right tool for you.

Regards,
Douglas
www.contigexpress.com

bioman1 · 07-31-2012, 07:29 AM

Thanks for reply. I have transcriptome assemblies with different treatments. I want to know which genes present in all treatments and what are all the genes that are absent in different treatments. I have tried tblastx ensembl (cDNA) insect sequence against transcriptome assemblies. Trying to find out highest coverage. Any suggestion?

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07-30-2012, 09:22 AM	#1
bioman1 Member Location: US Join Date: May 2012 Posts: 80	transcriptome assembly-comparative genomics I have three different transcriptome assemblies (Kmer 30,35 & 65) of one insect species. I want to compare transcriptome assemblies with reference insect sequence(from ensembl). I want to know how many genes show up in all kmer assemblies and between individual assemblies (i.e between 30 & 35, between 35 & 65). I would like to get idea to better way to compare to get list of genes. Any journal paper info regarding this will be helpful.

07-31-2012, 07:29 AM	#3
bioman1 Member Location: US Join Date: May 2012 Posts: 80	transcriptome assembly-comparative genomics Thanks for reply. I have transcriptome assemblies with different treatments. I want to know which genes present in all treatments and what are all the genes that are absent in different treatments. I have tried tblastx ensembl (cDNA) insect sequence against transcriptome assemblies. Trying to find out highest coverage. Any suggestion?

07-30-2012, 06:50 PM	#2
DZhang Senior Member Location: East Coast, US Join Date: Jun 2010 Posts: 177	Hi Bioman1, Can you share the purpose behind your proposed steps? Please look into whether CD-HIT is the right tool for you. Regards, Douglas www.contigexpress.com