Quality Control

Cutadapt to trim error text from fastq file

for better quality control.

Photo by Jonathan Borba on Unsplash

Install cutadapt by pip

pip install cutadapt

Check for error text and replace it accordingly to the output file.

cutadapt -a AACCGGTT -o output.fastq mutant_R1.fastq 
This is cutadapt 2.10 with Python 3.6.9
Command line parameters: -a AACCGGTT -o output.fastq mutant_R1.fastq
Processing reads on 1 core in single-end mode ...
[8<----------] 00:00:00 12,480 reads @ 6.1 µs/read; 9.81 M reads/minute
Finished in 0.08 s (6 us/read; 9.59 M reads/minute).
=== Summary ===Total reads processed: 12,480
Reads with adapters: 290 (2.3%)
Reads written (passing filters): 12,480 (100.0%)
Total basepairs processed: 1,872,000 bp
Total written (filtered): 1,870,988 bp (99.9%)
=== Adapter 1 ===Sequence: AACCGGTT; Type: regular 3'; Length: 8; Trimmed: 290 timesNo. of allowed errors:
0-8 bp: 0
Bases preceding removed adapters:
A: 29.3%
C: 21.4%
G: 15.9%
T: 33.4%
none/other: 0.0%
Overview of removed sequences
length count expect max.err error counts
3 236 195.0 0 236
4 44 48.8 0 44
5 9 12.2 0 9
83 1 0.2 0 1

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~~PEACE~~

A passionate automation engineer who strongly believes in “A man can do anything he wants if he puts in the work”.

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