HI there
I am sequencing ant bacterial communities and I have two runs: a 454 and a Miseq
The 454 run was last year and was done only in a few samples while the Miseq was performed recently in many samples (including resequencing the ones that I had sequenced with the 454)
Looking at the Otus, results are pretty consistent, after the analysis of the 454 run I had 180 Otus and basically the first 5 otus were the 97-98% of all reads while after the miseq run analysis I had 200 otus and again the first 5 otus were approximately the 97-98% of all reads
The 16S regions amlified in each run overlap (v3-v4 for the 454 and v4 (Kozich protocol))
I was trying to figure out a way to show which otu from the 454 corresponds to which otu from the 454
what I did was that I first run a get.oturep on both runs then took the fasta files and using blastn (with an 1e-50 cutoff) generated a list which shows me which otus from the 454 vs the Miseq have the best similarities
that seems to work almost ok and usually the top hit (or one of the top hits) from the blast search is the one corresponding to the right otu (for example by checking first the top hit of the blast search and then crosschecking if that makes sense in the heatmap (looking at the samples that I have sequenced both with 454 and Miseq) I was able to figure out that otu001 (454) is otu002 (Miseq) and otu 003 (454) is otu001 (Miseq) etc etc)
However as you can understand this is very tedious… so I was wondering if there is an easieÅ• way to do this?
any ideas and suggestions are welcome
thanks in advance
Panos
