Starting a FASTQ file

Note

These tutorials are still under active development.

Trimming a FASTQ file for both sequences and quality

Sometimes you might want to trim the reads, for example, removing UMIs and adaptor from the first 20 bp in R2.

from genomkit import GSequences
fastq = GSequences(name="R2", load=FASTQ_R2)
fastq.trim(start=20, end=0)
fastq.write_FASTQ(filename="R2_trimmed.fastq", gz=False)