Removing primers from Amplicon WGBS

Question

[Carlos]

Hello,

I have a FASTQ file of raw paired reads of whole genome bisulfite sequencing data of cfDNA. When running fastqc on my file I see the following in overrepresented sequences:

TTGGAGGCTCATCGTTCCTAGCTTGAGTATCTCGTATGCCGTCTTCTGCT 2692 0.24563590226027004 RNA PCR Primer, Index 26 (96% over 27bp)

CGTTGGAGGCTCATCGTTCCTAGCTTGAGTATCTCGTATGCCGTCTTCTG 1996 0.18212825442477673 RNA PCR Primer, Index 26 (96% over 25bp)

GTTGGAGGCTCATCGTTCCTAGCTTGAGTATCTCGTATGCCGTCTTCTGC 1971 0.17984708891344436 RNA PCR Primer, Index 26 (96% over 26bp)

What would be the proper command to trim the RNA PCR primers?

Thank you, Carlos

Answer 1

[GenoMax]

You can use fastp/bbduk.sh/cutadapt to remove any sequences you do not need.

Guide for bbduk.sh (use literal=sequence_you_want_to remove); https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/

fastp guide: https://github.com/OpenGene/fastp#simple-usage