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FastQC per base sequence content

I'm running FastQC on some paired-end fastq files. I have a warning on per-base sequence content, as the first 5 to 6 bases show significant bias towards T and G, as shown below. enter image description here I was wondering what the sequence in the first 5 or 6 bases is and whether I should trim it out before aligning with bwa.

per-base-sequence-content fastqc quality-control trimming
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updated by GenoMax GenoMax • written by Thanh • Thanh

1 answer

What kind of data is this? You can see this blog (likely applicable in your case): https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/

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written by GenoMax GenoMax

This is WES data with paired-end reads. Thank you for the reading! So I gather from this article that trimming the 5' end would be unnecessary for the downstream analysis, right?

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written by Thanh • Thanh

Correct. You can verify that by alignment stats.

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written by GenoMax GenoMax

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