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Old 08-01-2011, 02:22 PM   #1
Location: Missouri, USA

Join Date: May 2011
Posts: 16
Default About Insert, Insert size and MIRA mates.file

Hello All,
I am confused about what an Insert actually is ? And what is an insert size ?
I am dealing with 454 paired end data. How is a Linker different from an Adaptor?

I will be using MIRA's sff extract to extract the fasta and qual files from the sff files.
So does the sff files have read info this way:


i.e - Seq.forward - Linker - Seq.reverse ??

In the above, what is an insert ? and whats the size ?
So do each of the reads in an sff have the above format ?

So in the MIRA's mates.file setup can I just use the following default format for the mate pairs ?

pair (.*)\.f (.*)\.r

Please help me out with my confusions:


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Old 08-01-2011, 02:37 PM   #2
Location: Missouri, USA

Join Date: May 2011
Posts: 16

In addition, in the Newbler metrics of the assembly, for a particular sff file it says about the 'pairedReadStatus'
pairDistanceAvg = 2247.3
pairDistanceDev = 561.8

Now is this information about the assembly status or the raw reads status ?
Is pairDistanceAvg the Insert size ????
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