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Cutadapt&FastQC:sequence length disturbution failed after adapter trimming

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
disturbution cutadapt adapter trimming fastqc
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updated by dsull dsull • written by ashaneev07 • ashaneev07

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

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written by Bastien Hervé Bastien Hervé

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

enter image description here

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

enter image description here

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written by ashaneev07 • ashaneev07

1 answer

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.

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written by dsull dsull

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

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written by ashaneev07 • ashaneev07

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

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written by dsull dsull

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