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CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
https://reg-gen.readthedocs.io/
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Number of success in mpbs.bed and fulltest_statistics.txt files did not match #256

Open hhvu0102 opened 1 year ago

hhvu0102 commented 1 year ago

Hello,

I tested running RGT by running the example files from here (https://reg-gen.readthedocs.io/en/latest/motif_analysis/tutorial.html#full-site-test). Here are my commands:

rgt-motifanalysis matching --input-files input/regions_K562.bed input/background.bed --organism hg19
rgt-motifanalysis enrichment input/background.bed input/regions_K562.bed --organism hg19

From here there are two problems.

  1. I got the results file but the mpbs_ev.bed file was empty.

    wc -l enrichment/regions_K562/mpbs_ev.bed
0 enrichment/regions_K562/mpbs_ev.bed

    Did this mean my run was wrong?

  2. Number of success in mpbs.bed in the match folder and fulltest_statistics.txt files did not match.

    
head -n 2  enrichment/regions_K562/fulltest_statistics.txt

FACTOR P-VALUE CORR.P-VALUE A B C D FREQ BACK.FREQ. GENES MA0036.3.GATA2 1.3782e-02 1.0000e+00 59 299 57 458 16.48% [...]

Here, `A = 59`

grep MA0036.3.GATA2 match/regions_K562_mpbs.bed | wc -l 64


Did the match number got filtered somehow from the `match/regions_K562_mpbs.bed` file?

Thank you!