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Old 12-05-2012, 09:18 AM   #1
ryanmcg
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Default tool for mapping mobile elements?

Hi there

I'm specifically looking to map Ty elements in the yeast genome, but am also interested in mapping any other large scale changes (deletions, duplications, etc). I have paired-end Illumna data at about 150x coverage. I'm looking for the simplest way to do this. I have found one tool so far (VAMP), but it seems unnecessarily complicated to use. I have experience using Bowtie and Samtools to map SNPs, and was hoping to find something similar.

Any help would be appreciated.
Thanks!
Ryan
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Old 12-05-2012, 11:24 AM   #2
HESmith
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You can use the same strategy described in this publication. Basically, it involves remapping your reads against a transposon-only reference, filtering for reads where only one end aligns, then recovering the unique genomic alignment from the other read end.
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Old 12-06-2012, 07:55 AM   #3
ryanmcg
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Thanks for the suggestion. That looks like a good strategy. I do have paired end data, so it probably would make sense to utilize it though.
I think I found some other tools that might work.

Softsearch takes a very similar strategy to your method, but also augments it with paired-end data.
It seems relatively simple to use, though I will have to switch from Bowtie 1 to something else, maybe BWA.

I may also use RetroSeq. I think it may be better at finding Ty elements than Softsearch, or at least it would identify the Ty elements more quickly than sorting through the Softsearch results. I think I will also have to switch from Bowtie 1 for this.

I can't find any mention of what Bowtie 1 does with mate pairs that only align on one end. Are they thrown out completely, or flagged in some way?
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Old 01-16-2013, 10:02 PM   #4
RockChalkJayhawk
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Quote:
Originally Posted by ryanmcg View Post
Hi there

I'm specifically looking to map Ty elements in the yeast genome, but am also interested in mapping any other large scale changes (deletions, duplications, etc). I have paired-end Illumna data at about 150x coverage. I'm looking for the simplest way to do this. I have found one tool so far (VAMP), but it seems unnecessarily complicated to use. I have experience using Bowtie and Samtools to map SNPs, and was hoping to find something similar.

Any help would be appreciated.
Thanks!
Ryan
Ryan,
I wrote SoftSearch and would be happy to help if you're interested. I'm updating the website regularly with improvements, trying to get ready for paper submission, so make sure you use the latest version. Feedback is always welcome too.
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