Question about rCRSd and human_repeats

[hiroyukikato911]

Hi,

Previous version of PEPATAC pipeline denoted both rCRSd and human_repeats as prealignments.
prealignments: ['rCRSd', 'human_repeats']

as we can see from the following example.
http://pepatac.databio.org/en/latest/files/examples/tutorial/results_pipeline/tutorial2/PEPATAC_log.txt

However, the tutorial of the latest version only notes about rCRSd as shown here.
http://pepatac.databio.org/en/latest/run-container/

refgenie pull rCRSd/bowtie2_index

--prealignment-index rCRSd=default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4 \

What should I do with human repeats?
I would appreciate it if you could let me know:

1. Example code to pull from refgenie.

2. How to designate human repeats when running pepatac.py.

3. Also, I would appreciate it if you could clarify what would be the mm10 counterpart for rCRSd and human_repeats.
   (Is mouse_chrm2x sufficient?)

Finally, pypline version of example code is 0.9.6.
I think it would be helpful to every one if you could renew or also upload the example for Pipeline version: 0.10.0.
http://pepatac.databio.org/en/latest/files/examples/tutorial/results_pipeline/tutorial2/PEPATAC_log.txt

I'm a fan of this pipeline and I really appreciate your help.

Best regards,
Hiroyuki

[jpsmith5]

Hey @hiroyukikato911,

Yeah, I had just simplified the example but I internally always include human_repeats and it's a simple thing to keep including it on your end too.

1. To grab the asset with refgenie:

refgenie pull human_repeats/fasta human_repeats/bowtie2_index

2. An example using the test sample:

name: test_project

pep_version: 2.0.0
sample_table: test_annotation.csv

looper: 
  output_dir: pepatac_test/issue_203
  pipeline_interfaces: ../../project_pipeline_interface.yaml 

sample_modifiers:
  append:
    pipeline_interfaces: ../../sample_pipeline_interface.yaml
  derive:
    attributes: [read1, read2]
    sources:
      test_data_R1: "examples/data/{sample_name}_r1.fastq.gz"
      test_data_R2: "examples/data/{sample_name}_r2.fastq.gz"
  imply:
    - if: 
        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
      then: 
        genome: hg38
        prealignment_names: ["rCRSd", "human_repeats"]

Could save that in the pepatac/examples/test_project/ folder as, for example, test_config_refgenie2.yaml. Then from the parent pepatac/ direcotry run as: looper run examples/test_project/test_config_refgenie2.yaml. Be aware that in the current released version the prealignments flag is now prealignment_names due to the fact that the pipeline no longer explicitly requires refgenie, although that is still our recommended usage.

3. For mouse data, yes the mouse_chrM2x genome is the mitochondrial equivalent. We don't currently have a standard mouse repeat or satellite genome hosted on refgenie. If you had something local you wished to use in this context, we could walk you through the process of building a refgenie asset locally to represent the "mouse_repeats" type genome that you could then include.