Hi,
I tried trimmomatic and trimmed the reads down to 230 bp. I ran the following code:
qiime vsearch join-pairs --i-demultiplexed-seqs ITS_semifinal.qza --p-truncqual 12 --p-allowmergestagger --verbose --p-threads 4 --p-maxdiffs 30 --o-joined-sequences ITS_semifinal_merged.qza --output-dir ITSmerged
and got this output:
Merging reads 100%
56478 Pairs
13882 Merged (24.6%)
42596 Not merged (75.4%)
Pairs that failed merging due to various reasons:
33098 too few kmers found on same diagonal
9477 alignment score too low, or score drop to high
21 overlap too short
Here is the multiqc file of mean quality scores:
So trimming helped, but didnt finish the job.
Questions:
- Would trimming more off help?
- What other suggestions do you have?
- Does the most common error, ' too few kmers found on same diagonal' mean that the reads just arent similar enough to overlap??