Hello guys! I am triying to remove my primers from demultiplex paired end reads obtained from illumina MiSeq prior to run Deblur. First, I imported my data from a folder called Raw (this was ok) which contained foward and reverse fastq files as follows:
(qiime2-2018.6) [[email protected] Raw]$ time qiime tools import
Then I tried to trim my primers using cutadapt as follows:
cutadapt: error: Reads are improperly paired. Read name 'M03099:46:000000000-BBDY9:1:1101:22679:1783 2:N:0:107' in file 1 does not match 'M03099:46:000000000-BBDY9:1:1101:14264:1773 1:N:0:108' in file 2.
This was raised while processing sample11. The error is saying that your forward and reverse reads don’t match (the aren’t “paired” properly). Double-check your files, pre-import to QIIME 2 to make sure you imported what you intended to.
(Matthew Ryan Dillon)