Make.contigs question


I’m currently assembling some MiSeq data and I just had a general question about the make.contigs command. When I run it, I get a lot of warnings about the forward and reverse reads being a few bp different in length. When this is flagged, does mothur ignore the pair, or go head and try to combine them anyway? Due to the way the samples were prepared, we should have close to 200 bp worth of overlap between the forward and reverse so this difference won’t prevent the paired ends meeting, but will I be prematurely throwing away a large number of sequences simply because they don’t have equal length?

Are you using version 1.30.0 or 1.30.1? The only warnings about lengths in those versions should be if the sequence length does not match the the number of quality scores read. In that case mothur ignores the read.

This was in 1.22.something. I updated to 1.30.1 this morning and repeated it with no warnings, and managed to assemble a lot more contigs.

Plan for the future: when I see there’s a new version out, I won’t “just finish this thing first, then update”.