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VIB-PSB / MINI-AC

Motif-Informed Network Inference based on Accessible Chromatin (MINI-AC) is a method that combines accessible chromatin data from bulk or single-cell experiments with transcription factor binding site enrichment to learn gene regulatory networks in plants
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Fix second gene annotation #8

Closed hdbeukel closed 12 months ago

hdbeukel commented 12 months ago

This is the command that Nextflow used for network generation:

#!/bin/bash -ue
#bedops -e 50% zma_v4_genome_wide_motif_mappings.bed bundle_sheath_marand_top10k_3col.bed | bedtools closest -a stdin -b zma_v4_genes_coords_sorted.bed -t all -d -D b -k 2 > bundle_sheath_marand_top10k_peak_ann.bed

#bedmap --delim '   ' --fraction-either 0.5 --echo --skip-unmapped zma_v4_genome_wide_motif_mappings.bed bundle_sheath_marand_top10k_3col.bed | bedtools closest -a stdin -b zma_v4_genes_coords_sorted.bed -t all -d -D b -k 2 > bundle_sheath_marand_top10k_peak_ann.bed

#bedmap --delim '   ' --bp-ovr 5 --echo --skip-unmapped zma_v4_genome_wide_motif_mappings.bed bundle_sheath_marand_top10k_3col.bed | bedtools closest -a stdin -b zma_v4_genes_coords_sorted.bed -t all -d -D b -k 2 > bundle_sheath_marand_top10k_peak_ann.bed

bedmap --delim '    ' --echo --skip-unmapped zma_v4_genome_wide_motif_mappings.bed bundle_sheath_marand_top10k_3col.bed | bedtools closest -a stdin -b zma_v4_genes_coords_sorted.bed -t all -d -D b -k 2 > bundle_sheath_marand_top10k_peak_ann.bed

OMP_NUM_THREADS=1 python3 getNetwork_gw.py bundle_sheath_marand_top10k_peak_ann.bed bundle_sheath_marand_top10k_allshuff_sorted_miniac_stats.txt zma_v4_motif_TF_file.txt 0.1 bundle_sheath_marand_top10k_network_dups.txt --second_gene_dist 500

sort -u bundle_sheath_marand_top10k_network_dups.txt > bundle_sheath_marand_top10k_network.txt

Now --second_gene_dist 500 is included in the python command, as expected.