Not detecting the adapter in miRNAseq

[ndaniel]

It looks like FASTP is not able to detect automatically the adapter at all for miRNA-seq data.

For example, FASTP is not able to detect automatically the adapter in the SE FASTQ file from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR5087522

FASTP v0.19.6 was run as fastp -i SRR5087522.fq -o test.fq.

The first 3 input reads look like this:

@SRR5087522.1
TGTAACAGCAACTCCATGTGGAATGGAATTCTCGGGTGCCAAGAACTCCA
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJ
@SRR5087522.2
NAGCTTATCAGACTGATGTTGACTGGAATTCTCGGGTGCCAAGGAACTCC
+
#4BDFFFFHHHHHJJJJJJJJJJJJIJJJJIJIJCBHIJJJJJJJJJJJJ
@SRR5087522.3
NCCCGGCGGCTGGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACG
+
#1=DDFFFHHHHHJJJJJJJJIIJFGHHIJJIEHHHACDFFFFFEDADDD

FASTQC shows that this fastq file contains most likely the Illumina SmallRNA adapter 3', which according to FASTQC's database of adapters https://github.com/csf-ngs/fastqc/blob/master/Contaminants/contaminant_list.txt is this ATCTCGTATGCCGTCTTCTGCTTG.

According to Illumina official document: https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences-1000000002694-09.pdf these are all the Illumina small RNA adapters:

>Illumina Small RNA v1.5 3p Adapter
ATCTCGTATGCCGTCTTCTGCTTG
>Illumina RNA 3p Adapter (RA3)
TGGAATTCTCGGGTGCCAAGG
>Illumina RNA 5p Adapter (RA5)
GTTCAGAGTTCTACAGTCCGACGATC
>Illumina 5p RNA Adapter
GTTCAGAGTTCTACAGTCCGACGATC
>Illumina 3p RNA Adapter
TCGTATGCCGTCTTCTGCTTGT