Skip to content

Process

process [-h] [-a ADAPTER] [-g FRONT] [-b ANYWHERE]
                        [-c CUTOFF]
                        small_rna

positional arguments:
  small_rna             Path to FASTQ containing the small RNA

optional arguments:
  -h, --help            show this help message and exit
  -a ADAPTER, --adapter ADAPTER
                        Sequence of the adapter to remove from the 3' end
  -g FRONT, --front FRONT
                        Sequence of the adapter to remove from the 5' end
  -b ANYWHERE, --anywhere ANYWHERE
                        Sequence of the adapters to remove from both ends
  -c CUTOFF, --cutoff CUTOFF
                        Quality cutoff to trim RNA sequences at

Input files:

  • small_rna - fastq file containing raw RNA-seq data

Output files:

  • Fastqc/ - directory containing the raw output of FastQC

  • Trimmed_rna.fastq - file containing the raw RNA with adapters removed (only produced if an adapter sequence is provided)

  • Cut_sequences.fastq - sequences with low quality parts removed

Note that the parts of this step can easily be skipped. If you want to skip adapter trimming, don’t specify any adapters with -a, -g or -c. If you don’t want to run fastQC set -c 0. The program knows that in these cases, the steps do not have to be run.