analyis of single end data

Hi, I have some set of sequences where reverse reads are not good at all.
How can I use only R1 reads for my analysis, as make.contigs is not working with single reads columns.
Please suggest me the commands to use only single reads (R1).

I will follow your post with high interest, since I am facing the same issue.
Which regions did you target?
Here, we unfortunately selected V3V4, 2X300…

I’m afraid you’ll probably be limited to doing a phylotype-based analysis since the error rate climbs across the read. You may try trim.seqs with the quality control settings that were used with 454 data.


Hello Pat,

Do you mean process with the low-quality merged pair-end and do the trim.seqs on it? No way to do single-end analysis?

Thanks Pat! I will try your suggestion.

@nathali We also have V3V4 region