Analysis of 16S data and a PC or Unix computer

[stan1991]

Hi everyone,

I have got data for two regions of the 16S gene using Illumina MiSeq 2x250bp protocol but I am missing a large chunk of sequence from between the two reads. So there is no overlap. These reads have been taken from a mixed population. I don't want to have to analyse the two reads from a pair individually. Is there any way of linking the two reads from a pair together for data analysis? And what programs would everyone recommend for data analysis of 16S sequence for taxonomic assignment? I've been thinking about using QIIME or PANDAseq.

Also, would it make sense to generate a reference library containing just the sequence 250bp downstream of the two primer sites? The problem here might be that the reads are never 250bp long due to drop off in quality.

Thanks for reading and replying.

Stan

[bstamps]

One I'd ask what primer set you used, and what hypervariable regions you cross. You could artificially insert NNNNNNN between the reads (A bad idea in my opinion), though really you might be just as well off taking the forward read and analyzing that (http://nar.oxfordjournals.org/conten...e2=tf_ipsecsha). Use QIIME for the analysis- better, more integrated pipeline for actual analysis, whereas pandaseq would just assemble.

Hope that helps.