Very bad QC report

[tahamasoodi]

Hi,

I have a few whole genome samples with a very poor QC report as shown in the figures. Can I go for their further analysis or just discard them?

[DunderChief]

You have a ton of sequences with <3 for average quality. Remove these sequences, and re-run the fastQC. You may have enough sequences to salvage something.

[tahamasoodi]

Thanks, which tool shall i use to remove these sequences?

[westerman]

If paired end then use Trimmomatic. For single end you can get by with fastq_quality_trimmer. The latter is easier to set up. The latter can also be used with paired-end but this requires a lot more setup than Trimmomatic.

[westerman]

As a first pass, even if you have paired-end, you could treat the sample as single end thus running fastq_quality_trimmer just to see how many reads you end up with.