miRNA-seq Trimmomatic adapter file

Question

[inah]

Hi, what adapter file do I need to use to run Trimmomatic on miRNA-seq data generated on an Illumina Next-seq? I don't see any miRNA adapter file provided with Trimmomatic (or am I missing it), do I need to create one and how? Thanks, Ina

[GenoMax]

You could easily create one if you know what adapter sequences were used (what kit that was used to make libraries for your samples?).

[h.mon]

Use Trim_Gallore! with the --small_rna option, or use Trimmomatic with ILLUMINACLIP:<fastaWithAdaptersEtc>:, where fastaWithAdaptersEtc is the path to a fasta file containing adapter sequences - see the manual for more details.

edit: for Trim_Galore, check if the adapters used with the --small_rna are appropriate for your library kit prep, if not, pass the correct adapters with -a <ADAPTER SEQUENCE>.

[WouterDeCoster]

I have adapted your title to make it more explicit.

[inah]

To all who responded, thanks, I have tried to do what you suggested. Until now I have been using ea-utils mcf for adapter trimming and btrim for mild quality trimming (on mRNA, miRNA and total RNA). For mcf, I pass on an adapter fasta file provided by Illumina shown below. When I pass this file to Trimmomatic it does not recognize it and I am not sure how to modify it so it will work (after reading the manual). Thanks again, Ina

>miRNA_adapter
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC
>Illumina_adaptor
GATCGGAAGAGCGGTTCAGCAGGAATGCCGA
>Illumina_adaptor 2
AGATCGGAAGAGCGGTTCAGCAGGAATGCCGA
>Illumina_trueseq_universal
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina_PE_adaptor_13bases
AGATCGGAAGAGC
>Illumina_adaptor 1
GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
>Illumina adaptor 1 revers
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina PCR primer 1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina PCR primer reverse
CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
>Illumina DNA sequencing primer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Illumina PE adaptor 1
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>TruSeqUniversalAdapter
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>TruSeqAdapterIndex1
GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
>TruSeqAdapterIndex2
...
>TruSeqAdapterIndex27
GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTTTATCTCGTATGCCGTCTTCTGCTTG
>PEAdapter1
GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
>PEAdapter2
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PEPCRPrimer1.0
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PEPCRPrimer2.0
CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
>PERead1SequencingPrimer
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>PERead2SequencingPrimer
CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT

[GenoMax]

When I pass this file to Trimmomatic it does not recognize it

What exactly happens? This should be a plain text file and saved as such.

[Arindam Ghosh]

How about using the contaminant list supplied by FastQC as adapter list for trimmomatic? This helped me remove all contaminants that atleast FastQC can detect. I further combined this list with adopters supplied by Trimmomatic.