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Old 04-26-2013, 08:12 PM   #1
misagh
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Location: Los Angeles, CA

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Default Finding contig repeat counts by mapping contigs to the reference genome

Hi guys, I have a set of contigs of genome G (using de novo assembly by Velvet) and I also have the complete sequence of the reference genome G. I want to know the repeat count (an integer number) of each contig in the reality by mapping them to the reference genome and finding and counting exact matches.

Which tools are easier to use? At the moment I'm just interested to have a 2 column result, one column showing the contig names and the other showing an integer number which is the repeat count of that contig in the reference genome. Everything else is just a bonus. Would you please let me know which tool is better or how I can easily produce this result based on MUMmer or BLAST output?

Thanks.
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Old 01-09-2014, 05:41 AM   #2
bambus
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Hi,

I hope you would have got the solution for your query,if so can you please share it here as I too got stuck with the same problem.But,the only difference is that I am working with meta-transcriptomics data for which no reference genomes are available.So after assembly I mapped the original read file against the contig file and obtained an output in sam format.

Assemblers used:- SoapDenovo-Trans,Trinity,Metavelvet(didn't worked well with my data)
Mapping tools used :- Bowtie2,segemehl

It will be very helpful if you can post the procedure or steps you have gone through to get the desired information.

Thank you in advance.
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