What do these FastQC results mean?

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Hi @Sabsida

You could try a different trimming tool? You might need to input the custom adaptors used.

We have workflows that will enable you to review the FastQC and trimming tool reports all together.

More details are in this prior topic

So far, you know that this kit was used.

and that the reads ended up short, with adaptor detected at the end. This suggests that trimming with the automatic adaptors that Trimmomatic uses were not a match, and the trimming failed. You haven’t tried using CutAdapt or fastp yet. Both of those have an optional report that you can send to MultiQC. The example workflow above has an example that you can use as a template.

We can’t offer too much scientific advice at this forum (as @igor was clarifying) but we can help you to use the different tools in order to get all the results you might need for your own scientific review.

What to do:

  1. Start with the raw reads
  2. Determine what the original sequencing protocol was
  3. Applying the correct trimming
  4. Run FastQC again on the result
  5. Review the reports all together in MultiQC, make inferences, rerun until the data seems correct, then try the downstream steps.
  6. NOTE: When mapping to the human genome, you might be able to detect additional issues with the reads, in particular by reviewing the BAM inside of a genome browser like UCSC.

Hope this helps!