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I'm trying to use Taiji to run a pagerank on our combined bulk RNAseq and ATACseq dataset.

Here's how we run it:

taiji run --config config.yml -n 10

Here's config.yml:

input: "input.yml"
output_dir: "output2/"
assembly: "mm10"

Here's a snippet of input.yml (the real one has 8 conditions):

ATAC-Seq:
  - id: cond1_ATAC
    group: cond1
    replicates:
      - rep: 1
        files:
          - path: p1.cond1.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: p2.cond1.narrowPeak
            format: NarrowPeak
      - rep: 3
        files:
          - path: p3.cond1.narrowPeak
            format: NarrowPeak

  - id: cond2_ATAC
    group: cond2
    replicates:
      - rep: 1
        files:
          - path: p1.cond2.narrowPeak
            format: NarrowPeak
      - rep: 2
        files:
          - path: p2.cond2.narrowPeak
            format: NarrowPeak
      - rep: 3
        files:
          - path: p3.cond2.narrowPeak
            format: NarrowPeak

RNA-Seq:
  - id: cond1_RNA
    group: cond1
    replicates:
      - rep: 1
        files:
          - path: m1.cond1.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: m2.cond1.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: m3.cond1.tsv
            tags: ['GeneQuant']

  - id: cond2_RNA
    group: cond2
    replicates:
      - rep: 1
        files:
          - path: m1.cond2.tsv
            tags: ['GeneQuant']
      - rep: 2
        files:
          - path: m2.cond2.tsv
            tags: ['GeneQuant']
      - rep: 3
        files:
          - path: m3.cond2.tsv
            tags: ['GeneQuant']

We've checked that all the files are there. The NarrowPeak files were created by macs2, the tsv files are 2 column tsv's where column 1 is all EntrezID's we were measuring and column 2 is the expression of that gene.

The output of the pipeline is:

ATACseq
|-Download (empty directory
|-TFBS
| |-all narrowpeak files copied over in bed.gz format
| |-9 motif_sites_part.bed7411-?.gz (where ? is [0-8])
|-openChromatin.bed.gz (all peaks in the dataset)
GENOME (contains the mm10 genome)
RNAseq
|-All tsv files copied over
|-expression_profile.tsv (pasted all txv files together)
|-Download (empty directory)

The manual linked here says at the bottom there should also be two other files in the output directory, GeneRanks_PValues.tsv and GeneRanks.tsv. These are the only files we were looking for. Anybody have a clue why we don't see anything? Thanks.

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