Per sequence GC content still not good after trimming

Question

[zouini6]

I am analyzing NGS data for a prokaryotic genome and FastQC initially failed "Per sequence GC content". I then ran Trimmomatic on my Fastq files and after running FastQC on the trimmed paired dataset, the GC content is still not good. could someone tell me what is the reason for this?

The first .jnp shows the result I got before trimming and the second one is for after trimming.

Thank you

Answer 1

[GenoMax]

Is the organism you are working on GC rich? At this point in process I suggest that you move along with the analysis. If concerns crop up in dowstream analysis then you could revisit this to dig deeper.

There are no absolute failures with FastQC. Their appearence (red X) indicate that your data lies outside the defined bounds (which are for normal genomic sequencing).

[zouini6]

I don't know if it's a rich GC organism. I am moving along with the analyses but I just wanna know what are the potential interpretation for this because I'm supposed to comment and each step (with the results) for my assignment.

Thank you

[GenoMax]

A simple naive explanation can be that you have fragments in your data that contain more GC that most other fragments. That could simply be a by product of creation of libraries. At an extreme it could represent contamination by an unrelated genome.

[zouini6]

Thank you so much