Cutadapt&FastQC:sequence length disturbution failed after adapter trimming

Question

[ashaneev07]

Hi..,

I have data from clinical exome sequencing, and after adapter trimming, the sequence length distribution failed. It would be a great help if anyone knows why this happened? I used illumina universal adapter sequence fro trimming.

cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o sample34_R1_trimmed.fastq.gz -p sample34_R2_trimmed.fastq.gz sample34_R1.fastq.gz sample34_R2.fastq.gz

[Bastien Hervé]

Please provide an example of your input data, like a head of your fastq files, as well as your error message.

[ashaneev07]

Input format for trimmed fastq:

@SRR28522085.1 A00932:602:HCGMCDMXY:1:1101:14082:1047 length=150 GCTNTACCGCTTGTAGTCGAGAGCTGCATCCGTTACATCAATTTATATGGTAAGCTGGATCTTGGGCCAGTGTTTTCAGCAATCTGCAGAACAGGTGCTAGGCTGTTCTGATAGGAAATGAGATTCTAAAGATCGGAAGAGCACACGTCT + FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF @SRR28522085.2 A00932:602:HCGMCDMXY:1:1101:14425:1047 length=150 CGGNGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATCACACCACTACACTCCAGCCTGGGCGACAGAGTGAGAGTCTGCCTCAGACAAAAAAAAAAAAAGGAAAAAGAAACTAGTCCCTCAACCT + FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:,FFFFFFF,FFF:FFFFFFF @SRR28522085.3 A00932:602:HCGMCDMXY:1:1101:15474:1047 length=150 TTGNGCAAGGTAAGACAGACACTTCAGTGGATTTGTCCAGCCACCCTGCTTTGGGGAGGGGGTGGGACTTTTCTAATCGGCTGCCCTCGGTAGCGGACCCTGCATCAGTGCTCCTCGCCCTCCTGGGCCTTCCCCTCCCCGGGGGCCCTG +

Here is the sequence length distribution image

Thhis is the raw input fastq:

@SRR28522085.1 A00932:602:HCGMCDMXY:1:1101:14082:1047 length=150 GCTNTACCGCTTGTAGTCGAGAGCTGCATCCGTTACATCAATTTATATGGTAAGCTGGATCTTGGGCCAGTGTTTTCAGCAATCTGCAGAACAGGTGCTAGGCTGTTCTGATAGGAAATGAGATTCTAAAGATCGGAAGAGCACACGTCT +SRR28522085.1 A00932:602:HCGMCDMXY:1:1101:14082:1047 length=150 FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF @SRR28522085.2 A00932:602:HCGMCDMXY:1:1101:14425:1047 length=150 CGGNGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCTGAGATCACACCACTACACTCCAGCCTGGGCGACAGAGTGAGAGTCTGCCTCAGACAAAAAAAAAAAAAGGAAAAAGAAACTAGTCCCTCAACCT +SRR28522085.2 A00932:602:HCGMCDMXY:1:1101:14425:1047 length=150 FFF#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:,FFFFFFF,FFF:FFFFFFF

Answer 1

[dsull]

Well, of course it’s going to fail. A “success” would be that all sequences have the same length (151 bp). If you are trimming, many of your sequences will no longer have the same length (some may be 151 bp, some may be 130 bp, some may be 95 bp, etc.) hence the word “trimming”. The “success” vs “fail” of sequence length distribution no longer applies when you apply adapter trimming.

[ashaneev07]

So, I hope this doesn't affect the further analysis and results.

[dsull]

There is nothing to ‘hope’ for. If you understood my post, you’d know that it won’t affect any of your results.