I automatized my trimmomatic runs and it worked like a peach for 16S metagenomes.
However in my last run with transposases targeted metagenomes I found a problem for which I could not figure out the solution.
I had 24 paired end samples (24 x 2 fastqs) and trimmomatic processed only 13 (out of 24). I ran multiqC after trimmomatic results and it detected 13 logs.
This is the same basic command I had previously used for 16S a couple of times.
In the results folder there are 24 logs, but only 13 sequences were processed as 1P, 1U, 2P, 2U
trimmomatic_results.txt.
Before running trimmomatic I ran fastQC/multiQC and all 48 fastqs were analyzed, in which Nextera transposase adapters were recognized.
nana-marinbio
commented
2 years ago
I automatized my trimmomatic runs and it worked like a peach for 16S metagenomes.
However in my last run with transposases targeted metagenomes I found a problem for which I could not figure out the solution.
I had 24 paired end samples (24 x 2 fastqs) and trimmomatic processed only 13 (out of 24). I ran multiqC after trimmomatic results and it detected 13 logs.
My command to run trimmomatic was:
$cat mob_fqlist.txt | parallel -j 4 "trimmomatic PE -threads 5 mob-rawreads/{}_L001_R1_001.fastq mob-rawreads/{}_L001_R2_001.fastq -baseout mob-trimmomatic/{}.fq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:KeepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36 2> mob-trimmomatic/{}trimming.log"
This is the same basic command I had previously used for 16S a couple of times. In the results folder there are 24 logs, but only 13 sequences were processed as 1P, 1U, 2P, 2U trimmomatic_results.txt.
Before running trimmomatic I ran fastQC/multiQC and all 48 fastqs were analyzed, in which Nextera transposase adapters were recognized.
Any suggestions are welcome!