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Old 06-05-2008, 08:44 AM   #1
Kiki
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Default chromosome rearrangements

Hello there,

I'm thinking to do some paired-end sequencing on a 454. Do you know if the software that comes with the sequencer can identify chromosome rearrangements from the paired-end sequence or do we need to use the custom program.
Has someone done this type of work already? Any recommendations, tricks?

Thanks for you help,

Kiki
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Old 06-09-2008, 06:50 AM   #2
owomo
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The 454 assembly software can identify the paired-end information from the reads, but what you mean chromosome rearrangements ?
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Old 06-09-2008, 07:59 AM   #3
Kiki
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Default chromosome rearrangements

Hello,
By chromosome rearrangements, I mean the cases where both paired-end sequences, don't match the reference genome sequence at the same place.
For example one paired-end sequence matches on the expected location but the other paired-end sequence matches on another chromosome and on the same chromosome but much further away than expected. In these cases, we have a translocation and an insertion, respectively.
I talked to a 454 rep and it seems that the software doesn't do that and that we need a custom program to parse the paired-end sequencing data.
Has someone done this type of work?

Cheers.
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Old 06-15-2008, 05:06 AM   #4
owomo
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That‘s interesting.
As i know,Each 454 Long Paired End Sequencing reads contains a mate paired_end information, and the distance between a mate pair is about 3kb. So you can split a paired_end read into two parts, then seach from the reference genome one by one using blast, if one of the two parts can matches the genome more than one, then probably we got a insertion. And if the two parts can match two different genome, we got a rearrangements.

Last edited by owomo; 06-15-2008 at 05:28 AM.
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Old 11-06-2008, 08:55 PM   #5
glacerda
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You could use cross_match to detect the 44mer linker sequence and then use some perl to split the read into mates. Then you can use nucmer to map mates to the reference genome.

PS: I have noted that most linker sequences in 3K-LT PE are not exactly 44mer. They are in the range from 20-80 bp

Besides that, you will have to discard reads in which the mates (fragments before and after the linker) are shorter than a specified cutoff (I use 22bp).
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