[mira_talk] Re: fn in paired-end reads?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 31 May 2011 22:06:22 +0200
On Tuesday 31 May 2011 16:43:47 Cleo HC Ho wrote:
> Thanks a lot! May I ask where you obtain this documention? I couldn't find
> it on the sff_extract website.
My bad. I wrote the code for the paired-end splitting but somehow missed to
coordinate with Jose regarding updating the docs.
I remember that the question about read naming already came up earlier on the
talk list and I'd made a note somewhere to take this up, but ... another thing
I've missed.
> Also, why does the reverse read have be written in complement? Aren't the
> right and left sides of the linker from the same strand of DNA?
Long story short: when I wrote this, I wanted to test a number of assemblers
with the data. Those who did not know 454 yet I declared the reads to be
"Sanger" and with those the algorithms expect to have one forward and one
reverse read.
It also saved me some ten to twenty lines of code in MIRA to teach it that
some sequencing methods have read pairs in "forward-forward" orientation ...
which I added a couple of months later anyway.
Which brings me to: anyone reading this thread who has an oppinion whether I
should change the default behaviour of sff_extract to not reverse one of the
reads (and have MIRA also use forward-forward as default expectation in 454
paired-ends)?
B.
Other related posts:
