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 times
No. 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

Thanks for reading my post.

~~PEACE~~