Question: Identify informative markers from two in silico digests?
0
gravatar for J.R.
4.4 years ago by
J.R.0
United States
J.R.0 wrote:

Hi all,

I'm trying to analyze fragments generated from in silico digests of two draft genomes to determine how many of the fragments differ between the two species. For input, I have two unordered lists of ~5,000 ~300bp fragments (one from each species); I would like to determine how many of them are identical, how many differ by 1 base, 2, 3, etc., and how many don't have a corresponding fragment in the other genome.

Is this possible? What approach should I take? I can't seem to figure out if pairwise aligners will handle unordered lists like this, or if multiple alignment is what I need, or if I just want to map both sets back to one of the reference genomes. I'm not very experienced at this but I'd like to learn.

Thanks,

Joanna

dna snp alignment in silico rad-seq • 1.0k views
ADD COMMENTlink modified 4.4 years ago by Biomonika (Noolean)3.1k • written 4.4 years ago by J.R.0
1
gravatar for Biomonika (Noolean)
4.4 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

I would try clustering them as a first quick shot, so I would first make sure that the header names are distinct in these two groups, then used for example CD-HIT (http://weizhongli-lab.org/cd-hit/) and parsed the clusters I would get (proportion of sequences in group 1 versus group 2 in each cluster). Also, sizes of the clusters would be interesting to look at. (I guess that if clustering worked well, I would sort clusters by length and then plot proportions as very narrow barplots with two colors representing groups. But that's very personal suggestion :D)

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Biomonika (Noolean)3.1k

Thank you! That ended up working really well, and the output was super-easy to parse. Thanks so much!

ADD REPLYlink written 4.3 years ago by J.R.0

Glad to here that! Please remember to upvote my (and any other) answers that you find helpful ;-)

ADD REPLYlink written 4.3 years ago by Biomonika (Noolean)3.1k

Thanks! Always good to learn the etiquette of new online communities :D

ADD REPLYlink written 4.3 years ago by J.R.0
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