Got different node weight when switched the expression files

[avialee]

Hi,

I am running Taiji on our ATAC-seq and RNA-seq data of WT and KO samples. We have two repeats on each type of data. Actually we already got the peak files from ATAC-seq and expression matrix from RNA-seq using our own pipeline. So I fed Taiji with peak files and expression files. However when I switched the 2 repeats of expression files in the input.yml file, I got different values in the nodes.csv. I have no idea how the weight of nodes is calculated. They should be same even the repeat file is switched, right?

Thanks.

[kaizhang]

Could you show me the changes you had made in the input.yml file?

[avialee]

ATAC-seq part is the same, only RNA-seq part is changed:

Before switched: ATAC-seq:

• id: WT_atac group: WT replicates:
  • rep: 1 files:
    • path: VWT.SI_peaks.narrowPeak format: NarrowPeak
• id: KO_atac group: KO replicates:
  • rep: 1 files:
    • path: VKO.SI_peaks.narrowPeak format: NarrowPeak

RNA-seq:

• id: WT_rna group: WT replicates:
  • rep: 1 files:
    • path: expression_SI_wt1.tsv tags: ['GeneQuant']
  • rep: 2 files:
    • path: expression_SI_wt2.tsv tags: ['GeneQuant']
• id: KO_rna group: KO replicates:
  • rep: 1 files:
    • path: expression_SI_ko1.tsv tags: ['GeneQuant']
  • rep: 2 files:
    • path: expression_SI_ko2.tsv tags: ['GeneQuant']

After switched:

ATAC-seq:

• id: WT_atac group: WT replicates:
  • rep: 1 files:
    • path: VWT.SI_peaks.narrowPeak format: NarrowPeak
• id: KO_atac group: KO replicates:
  • rep: 1 files:
    • path: VKO.SI_peaks.narrowPeak format: NarrowPeak

RNA-seq:

• id: WT_rna group: WT replicates:
  • rep: 1 files:
    • path: expression_SI_wt2.tsv tags: ['GeneQuant']
  • rep: 2 files:
    • path: expression_SI_wt1.tsv tags: ['GeneQuant']
• id: KO_rna group: KO replicates:
  • rep: 1 files:
    • path: expression_SI_ko2.tsv tags: ['GeneQuant']
  • rep: 2 files:
    • path: expression_SI_ko1.tsv tags: ['GeneQuant']

[kaizhang]

There shouldn't be any differences. In the RNASeq directory, there is a file named expression_profile.tsv. Please check whether the file stays the same between the two runs.

[avialee]

Here are the fist a few lines in expression_profile.tsv, it is also switched:

before switched: WT WT KO KO Ubl5 565.0413975 670.3987042 558.0231156 736.6467091 Gm38348 0.0 0.0 2.783157684 0.0 Ttc32 77.0089261 73.81095833 73.75367862 89.25241697

after switched: WT WT KO KO Ubl5 670.3987042 565.0413975 736.6467091 558.0231156 Gm38348 0.0 0.0 0.0 2.783157684 Ttc32 73.81095833 77.0089261 89.25241697 73.75367862

[kaizhang]

I see. This is probably a bug (Taiji-pipeline/Taiji-RNA-seq#1) introduced in v1.1.0. I will fix it this weekend.

[avialee]

Thanks!

[kaizhang]

Fixed in v1.2.1.