How to detect adaptors when Galaxy fails to identify adaptors?

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1

My miRNA fastq files read as follows:

;>SRR1658346.1 HISEQ1:187:D0NWFACXX:3:1101:2565:2050 length=51
ATCATACAAGGACAATTTCTTTTAACGTCGTATGCCGTCTTCTGCTTGNAA
>SRR1658346.2 HISEQ1:187:D0NWFACXX:3:1101:2654:2232 length=51
TCGAGGAGCTCACAGTCTAGTATAACGTCGTATGCCGTCTTCTGCTTGAAA
>SRR1658346.3 HISEQ1:187:D0NWFACXX:3:1101:2870:2103 length=51
TTCAAGTAATCCAGGATAGGCTAACGTCGTATGCCGTCTTCTGCTTGAAAA
>SRR1658346.4 HISEQ1:187:D0NWFACXX:3:1101:3001:2147 length=51
TAGCACCATCCGAAATCAGTTTAACGTCGTATGCCGGCTTCTGCTTGAAAA

The second sequence is probably my adaptor sequence:

ATCATACAAGGACAATTTCTTT TAACGTCGTATGCCGTCTTCTGCTTGNAA
TCGAGGAGCTCACAGTCTAGTA TAACGTCGTATGCCGTCTTCTGCTTGAAA
 TTCAAGTAATCCAGGATAGGC TAACGTCGTATGCCGTCTTCTGCTTGAAAA
 TAGCACCATCCGAAATCAGTT TAACGTCGTATGCCGGCTTCTGCTTGAAAA

But on doing FastQC and MultiQC, “No samples found with any adapter contamination > 0.1%” this message is displayed.

The individual FASTQC file however predicted the occurrence of Adaptor:

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Untitled1238Ă—1260 71.2 KB

What is the way out?
Is the alignment of the sequence wrong? Is it supposed to start with the adaptor sequence? So should I rewrite the fastq files?

2

Hi @Sanjukta_Ghosh

You could try using a trimming tool, and see if that removes the adaptors.

Run FastQC before and after, then compare.

If you are curious about what the different FastQC modules do, scroll down on the tool form and click into the author’s resources. They have examples with explanations.

More help is in the Galaxy tutorials. Start here: https://training.galaxyproject.org/training-material/search2?query=quality

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