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-   -   how to align the contigs to the reference genome (http://seqanswers.com/forums/showthread.php?t=19704)

jjjscuedu 05-01-2012 11:27 AM

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

seb567 06-05-2012 08:39 AM

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

Quote:

Originally Posted by jjjscuedu (Post 72276)
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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