Skip to content

Running Trim

Basic Configuration

Trim requires a file of untrimmed small RNAs and the adpaters to trim - either explicitly or through the kit used - to be specified. Examples of config files for possible usage is as follows.

Trimming adapters with the 5' sequence ACGTTTAGAT and the 3' sequence GCTAGGATA:

smallRNA_fastq: smallrna_untrimmed.fastq
trim:
  5_prime: ACGTTTAGAT
  3_prime: GCTAGGATA

Trimming adapters from the qiagen kit in forward direction:

smallRNA_fastq: smallrna_untrimmed.fastq
trim:
  kit: qiagen

Trimming adapters from the qiagen kit in reverse direction:

smallRNA_fastq: smallrna_untrimmed.fastq
trim:
  kit: qiagen-rev

Currently the valid values for kit are:

  • qiagen - qiagen kit, forward direction
  • qiagen-rev - qiagen kit, reverse direction
  • neb - NEB kit, forward direction
  • neb-rev - NEB kit, reverse direction

Once this config is written, it can be run as usual using:

$ hlsmallrna config.yml

Tip

Remember if you install via apptainer or docker you will need to prepend the command from the install page. For apptainer this command becomes: 

$ apptainer run -B $HOME:$HOME hlsmallrna.sif hlsmallrna config.yml

Optional Parameters

min_quality

This sets the quality cutoff in cutadapt when filtering low quality ends. Defaults to 20 - example below sets it to 15:

trim:
  ...
  min_quality: 15

Output Files

trimmed_reads.fq

This is a FASTQ file containing all the trimmed reads that passed the filters of quaility and had a 3' adapter present.