something about paired-end read

[huanggm]

hi all,
I am a newer in here,and just start read some paper about paird-end-read.I confuse about something.

"This gives you the ability to map to a reference (or denovo for that matter) using that distance information. It helps dramatically to resolve larger structural rearrangements (insertions, deletions, inversions), as well as helping to assemble across repetitive regions" this sentences come from http://seqanswers.com/forums/showthread.php?t=503,I can't understand completely.

what does the "insertions, deletions, inversions" mean,for example, the "deletion" refer to the region where we can't read when we read the two end of a genome?is that right,who can explain for me.

thanks very much!

[Lluc]

Some basics: one thing is to re-sequence and then map the reads to the reference genome, and another thing is de novo sequencing and assembly. Paired-end mapping helps both. In the first application, the information of the distance between the ends can be used either to find the correct mappings of each end, or to discover structural differences between the sequenced genome and the reference genome. To understand better how you do the latter, you can read any of several reviews about structural variation detection with paired-end mapping data. For example,

http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1374.html

[huanggm]

Some basics: one thing is to re-sequence and then map the reads to the reference genome, and another thing is de novo sequencing and assembly. Paired-end mapping helps both. In the first application, the information of the distance between the ends can be used either to find the correct mappings of each end, or to discover structural differences between the sequenced genome and the reference genome. To understand better how you do the latter, you can read any of several reviews about structural variation detection with paired-end mapping data. For example,

http://www.nature.com/nmeth/journal/...meth.1374.html

thanks,i will review

[maria.b]

Hi huanggm,

this sentence means that paired end read may help you to discover structural variation. If your sample has a deletion of a particular region compared to the reference, the insert size of the pairs which mapped that region will be smaller than expected. For insertion the insert size will be longer or you will be able to map only one read of the pair, for inversion the orientation of the read inside the pairs will be different.

Maria

[huanggm]

Hi huanggm,

this sentence means that paired end read may help you to discover structural variation. If your sample has a deletion of a particular region compared to the reference, the insert size of the pairs which mapped that region will be smaller than expected. For insertion the insert size will be longer or you will be able to map only one read of the pair, for inversion the orientation of the read inside the pairs will be different.

Maria

thanks for your explain,i can understand this notion much better!