RadSeq and short read
0
0
Entering edit mode
2.4 years ago
gbl1 ▴ 80

Hello,

I have some RadSeq sequences from illumina sequencing. I have got my traditional R1 and R2 and I try to find out all fragment I might use for clustering. I used FLASH in order to assemble the fragments with matching ends:

.|<---------

.        ---------->|

I'm not interested in outies for now:

.     |<----------

---------->|

What I miss is the full elements:

|<-------->|

Knowing the primers at both ends, is there a way to extract all the fragments that are fully sequenced from both sides?

Thanks in advance,

Benjamin

RadSeq Illumina Clustering • 386 views
ADD COMMENT
0
Entering edit mode

What is the objective of the RADseq project you are working on? Might I suggest STACKS (http://catchenlab.life.illinois.edu/stacks/) or ipyrad (https://ipyrad.readthedocs.io/) or dDocent (http://www.ddocent.com/) for the analysis?

ADD REPLY
0
Entering edit mode

I try to compare several individuals on presence/absence of all sequences.

I'll have a look at your programs

Thanks

ADD REPLY

Login before adding your answer.

Traffic: 1452 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6