Hello all. I am using FastQC from Babraham Bioinformatics to analyze Illumina RNAseq output (fastq.gz).
For an older set of data, I get beautiful box plots...yellow upper and lower quartile boxes, red mean lines, tails in both directions. Everything is in the green zone (high oh red quality). These data were given to me back when the sequencing core had personnel to run QC and trimming before sending us data.
Recently, I got data where the box plots only have red mean bars, no yellow boxes (everything is in the green zone...high quality). Statistically, this is strange. This time the core facility did not process the data at all before sending it to me.
The adapter content shows signal at the last 20 base pairs of the reads.
Why would my reads have means with no variation in the quality score? Does this mean my reads are all adapters?
Thank you.
Is it possible to add a screenshot to make the question more clear?
Based on text alone, it sounds like all your reads are just very good quality, which is not surprising. Here is a related discussion: Fastq files with very high per base sequencing quality score
Here is a sreenshot:
https://postimg.org/image/tl6gyv1an/
That looks fine. The data appears to be pre-trimmed.
Probably nothing to worry about. As technology has matured the Q-scores for good libraries can be uniformly high across the cycles (leading to no visible yellow boxes).
As for the adapters they may be present in some reads (so be sure to scan/trim the data) but the bases there may also have high Q scores.