SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Insert size important? 454andSolid De novo discovery 3 12-27-2017 02:33 AM
unexpected insert size eren Illumina/Solexa 2 08-24-2011 08:27 AM
Insert size for Pindel mard Bioinformatics 0 12-15-2010 09:08 PM
insert size polystone Sample Prep / Library Generation 0 05-04-2010 11:07 AM
insert size adrian Bioinformatics 1 03-18-2010 05:55 PM

Reply
 
Thread Tools
Old 08-01-2011, 02:22 PM   #1
aarthi.talla
Member
 
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:

|-----75----|------------------------100-----------------|-----75-----|

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:

Thanks

Aarthi
aarthi.talla is offline   Reply With Quote
Old 08-01-2011, 02:37 PM   #2
aarthi.talla
Member
 
Location: Missouri, USA

Join Date: May 2011
Posts: 16
Default

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 ????
aarthi.talla is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:01 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO