I have a set of isolates sequenced with MiSeq (Nextera XT DNA, paired-end reads, 600 cycles). However, the MiSeq samples suffered a major quality drop from the 150 to the 300 cycle, and from the 450 to the 600 cycle, probably due to a problem with the MiSeq reagent kit v3 lot.
The coverage I get for this samples, using samtools, goes from 28x to 80x. I would like to improve the coverage of this samples and thus I tried to cut the raw reads after the first 150 bp using the Trimmomatic CROP option:
§ java -jar trimmomatic-0.36.jar PE -threads 8 -trimlog input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 CROP:150
I have also tried fastx_trimmer:
§ fastx_trimmer -l 150 -z -i INFILE -o OUTFILE
Unfortunately, I am not able to greatly improve the coverage. Do you think I should use other trimming options? Any suggestions?