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Old 05-01-2012, 11:27 AM   #1
jjjscuedu
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Location: NY

Join Date: Mar 2012
Posts: 35
Default how to align the contigs to the reference genome

Hi all,

I am trying to do the de-novo assembly for my RNAseq dataset. First, I want to compare the accuracy of different assembly tools.

Hence, I select one RNAseq data which already a reference genome.

And we have assembly many different transcripts/contigs.

Now, I want to check where these contigs coming from the chromosome and how many contigs can be aligned to the chromosome.

For this questions, can anyone give me some suggestions about which tools is applicable?
Because the length for the contigs/transcipts is much longer than the original reads, how any mismatch I should set for the alignment?

Thanks!

Jingjing
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Old 06-05-2012, 08:39 AM   #2
seb567
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Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

MUMmer is the a definite tool for mapping assemblies onto references.

Quote:
Originally Posted by jjjscuedu View Post
Hi all,

I am trying to do the de-novo assembly for my RNAseq dataset. First, I want to compare the accuracy of different assembly tools.

Hence, I select one RNAseq data which already a reference genome.

And we have assembly many different transcripts/contigs.

Now, I want to check where these contigs coming from the chromosome and how many contigs can be aligned to the chromosome.

For this questions, can anyone give me some suggestions about which tools is applicable?
Because the length for the contigs/transcipts is much longer than the original reads, how any mismatch I should set for the alignment?

Thanks!

Jingjing
seb567 is offline   Reply With Quote
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