Configure UMI settings

By default, the pipeline assumes there is not a UMI. In other words, the parameter umi_len is set to 0. See the pipeline usage documentation for additional parameter settings.

Specify a UMI length

There are three approaches for specifying the umi_len parameter for your samples.

1: Pass the --umi-len parameter at the command line

If you're running PEPPRO at the command line for a single sample, you may specify the UMI length using the --umi-len argument.
For example:

./pipelines/peppro.py \
  --sample-name test \
  --genome hg38 \
  --input examples/data/test_r1.fq.gz \
  --single-or-paired single \
  --umi-len 8 \
  -O $HOME/peppro_example/

2: Pass the --umi-len parameter to the pipeline using looper

If you're running PEPPRO with looper, you can also pass any number of additional arguments to looper that will be automatically passed to the pipeline.
For example:

looper run examples/meta/peppro_test.yaml -d \
  --compute slurm \
  --umi-len 8

In this case, looper will automatically pass the --umi-len 8 argument to each sample in the peppro_test.yaml file.

3: Specify a --umi-len argument in the project configuration file

If you're using looper and you'd like to set the --umi-len for individual samples that is entirely possible with some customization to the configuration and annotation files. For a real life example, check out the peppro_paper.yaml and peppro_paper.csv project files.

Below we'll go over two examples of customization in the project configuration files.

1: Set a universal --umi_len in the project configuration file

# Run test sample through PEPPRO
name: test

metadata:
  sample_annotation: "peppro_test.csv"
  output_dir: "$PROCESSED/peppro/peppro_test/"
  pipeline_interfaces: "$CODE/peppro/pipeline_interface.yaml" 

derived_columns: [read1]

data_sources:
  R1: "$CODE/peppro/examples/data/{sample_name}_r1.fq.gz"

implied_columns:
  organism:
    human:
      genome: hg38
      prealignments: human_rDNA
      adapter: cutadapt  # Default
      dedup: seqkit      # Default
      trimmer: seqtk     # Default
      protocol: pro      # Default
      umi_len: 8         # Custom --umi-len that will be passed to **all** samples
      max_len: -1        # Disable length trimming 

pipeline_args:
#  peppro.py:
#    "--prioritize": null # Default is FALSE. Pass flag to prioritize features by the order they appear in the feat_annotation asset when calculating FRiF/PRiF
#    "--sob": null        # Default is FALSE. Pass flag to use seqOutBias for signal track generation and to incorporate mappability
#    "--scale": null      # Default is FALSE. Pass flag to scale seqOutBias signal tracks
#    "--coverage": null   # Default is FALSE. Pass flag to use coverage when producing library complexity plots.
#    "--keep": null       # Default is FALSE. Pass flag to keep prealignment BAM files.
#    "--noFIFO": null     # Default is FALSE. Pass flag to NOT use named pipes during prealignments.
#    "--complexity": null # Default is TRUE.  Pass flag to disable library complexity calculation. Faster.

2: Set custom --umi_len arguments for individual samples

What do you do if your project doesn't have the same UMI for all samples? This requires a bit more complexity. Our paper's samples do exactly this, and you can go check out those configuration files specifically for complete detail. Here we'll highlight the relevant components.

In our paper' project configuration file we use the implied_columns feature to create custom arguments based on our corresponding annotation file. We can include any column of choice, in this case we call it umi_status, that includes multiple possible matches. If a sample includes true_8 in the umi_status column, we will pass a --umi-len 8 to the pipeline. Conversely, if a sample includes true_6 in the umi_status column, we will pass a --umi-len 6 to the pipeline. If neither argument is present, we use the default setting of length 0.

Here's a snippet of the relevant portion of the configuration files:

  • configuration file
 umi_status:
    true_8:
      umi_len: 8
    true_6:
      umi_len: 6
  • annotation file
umi_status
FALSE
FALSE
true_6
true_8
true_8