Per tile sequence fails after trimming

Question

[ijarne]

Hi,

I performed trimming on some fastq that I will use for Whole Exome Sequencing (WES) analysis. After trimming using bbduk:

$bbduk -Xmx1g in1="${pair}_R1_001.fastq.gz" in2="${pair}_R2_001.fastq.gz" out1="${CURRENT_DIRECTORY}/1_trimming/${pair}_1_trimmed.fastq.gz" out2="${CURRENT_DIRECTORY}/1_trimming/${pair}_2_trimmed.fastq.gz" ref="${adapters}" ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=20 minlen=35 stats="${CURRENT_DIRECTORY}/1_trimming/${pair}_trimming_stats.txt" refstats="${CURRENT_DIRECTORY}/1_trimming/${pair}_trimming_refstats.txt"

I discovered that the profile of my sequences changed from the image on the left to the image on the right. With the code I used I expected the results I have in the "Per base Quality", "Per sequence quality scores" and "Sequence Length Distribution" graphs (that I am not providing here). Nevertheless, I just discovered this "strange profile" in the "Per tile sequence quality", this is a problem I had never faced to be honest.

Almost all my samples look like this so my question is whether if you'd do something else or you would proceed with the analysis.

Thanks !

Answer 1

[GenoMax]

I suggest you proceed with the analysis. Any oddities like this should be managed by the aligner. If you start seeing any strangeness then backtrack to investigate more.