No matter how i trimmed the drop in quality of the R2 reads could not be dealt with.
I tried changing the slidingwindow settings as well as trimming of between 2-32 bases from the tail.
In the end, these where the optimal settings.
fastp -c -f 4 -t 2 -F 4 -T 2 -r -W 4 -M 27 -l 36
-c: corrects mismatched base pairs in overlapped regions of paired-end reads.
-f 4 -t 2: Four first bases and the two last bases are trimmed off for R1.
-F4 -T 2: Four first bases and the two last bases are trimmed off for R2.
-r -W 4 -M 27: Slidingwindow with a window size of 4 and mean quality threshold of Q27.
-l 36: reads shorter than 36 are trimmed off.
The trimming was automated with fastp_trim.sh.
In submission/ the multiqc reports for fastp, fastqc raw and fastqc trimmed can be found.
No matter how i trimmed the drop in quality of the R2 reads could not be dealt with. I tried changing the slidingwindow settings as well as trimming of between 2-32 bases from the tail. In the end, these where the optimal settings.
fastp -c -f 4 -t 2 -F 4 -T 2 -r -W 4 -M 27 -l 36-c: corrects mismatched base pairs in overlapped regions of paired-end reads.-f 4 -t 2: Four first bases and the two last bases are trimmed off for R1.-F4 -T 2: Four first bases and the two last bases are trimmed off for R2.-r -W 4 -M 27: Slidingwindow with a window size of 4 and mean quality threshold of Q27.-l 36: reads shorter than 36 are trimmed off.The trimming was automated with
fastp_trim.sh.In
submission/the multiqc reports for fastp, fastqc raw and fastqc trimmed can be found.