making sure redundans sends all libraries into the scaffolding steps

[Richards, Stephen]

Hi Leszek and everyone, 

I am trying to run redundans on some really terrible assemblies in hopes of improving them.

However not all of the libraries - especially the 8kb mate pair libraries are being used in scaffolding steps, 

I presume because the code says they are too bad - although it is possible that the contigs are so small that estimation of 

insert sizes is terrible, which makes the libraries look worse than they really are.

I would like to tell redundans to use these libraries in scaffolding and gap closure anyway, 

Can you give me some hints about how the python code makes these decisions, and how I might best over-ride them

to say use this library anyway?

Cheers, 

fringy

Stephen Richards
Associate Professor

Human Genome Sequencing Center
Baylor College of Medicine
N1501, One Baylor Plaza, 
Houston TX 77030

step...@bcm.edu
work 713 798 6667

[lech...@gmail.com]

Hi Fringy! 

Good to hear from you :) 

You can set insert size info by manually. 

If you somefile_R1.fq and somefile_R2.fq and you want mate-pairs with RF orientation and 5kb insert size +/- 1.5kb, create somefile_R2.fq.is.txt with below information (read_length, median_IS, mean_IS, stdev, FF, FR, RF, RR)

60  5000.0        5000.0  1500.0  0       0      100000   0

Bests, 

L. 

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