Using cutadapt for primers


I’ve been using cutadapt to remove primers before running make.contigs on my Miseq data due to some problems using the inbuilt commands in mothur. Cutadapt removes sequences which do not contain the primer (with an allowed 10% error) from the original file. This has meant that when running make.contigs I get lots of the following error messages:
[WARNING]: did not find paired read for MISEQ-01:97:000000000-A5ARF:1:2114:9979:27893, ignoring.

I know why this occurs but I was wondering whether this would cause any problems due to file formatting etc.?



It shouldn’t. There is a preprocessing step in the make.contigs command. This is were mothur checks for pairs, errors in the fastq files and divides the reads between the processors. Any reads that don’t have pairs are not passed along to the processing step.