Config file setup example for paired end and replicates

Issue #76 new
Former user created an issue

Is there an example config.yaml file I can look at which tells me how to correctly setup my paired end files and deal with replicates please? I can't understand what format is required from the tutorial pages. Here's what I'm currently trying:

# ATTENTION: You should and only should choose one type of input file between "samples" and "counts".
# Configuration of samples (Cannot set "counts" as valid at the same time!)

samples:
    # The following sample information was inferred from the given FASTQ files.
    # Adjust it according to your needs (e.g. providing descriptive sample names and grouping replicates together).
    A.day0:
        - /reads/Sample_1_1.fastq.gz
        - /reads/Sample_1_2.fastq.gz
    A.day7_1:
        - /reads/Sample_3_1.fastq.gz
        - /reads/Sample_3_2.fastq.gz
    A.day7_2:
        - /reads/Sample_4_1.fastq.gz
        - /reads/Sample_4_2.fastq.gz
    A.day14_1:
        - /reads/Sample_7_1.fastq.gz
        - /reads/Sample_7_2.fastq.gz
    A.day14_2:
        - /reads/Sample_8_1.fastq.gz
        - /reads/Sample_8_2.fastq.gz


# Provide paired fastq files if pair-end sequencing data is available.
# paired:
#     # provide a label and a paths to the paired fastq files for each sample
#     A: path/to/A_R2.fastq
#     B: path/to/B_R2.fastq
#     C:
#        - path/to/C.1_R2.fastq
#         - path/to/C.2_R2.fastq

Comments (1)

  1. Owen Chapman

    Same issue. Is MAGeCK-VISPR being actively maintained? I see a few issues like this unresolved.

  2. Log in to comment