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jvanheld
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IBIS_2024
Participation to the IBIS nebchmarking for motif discovery approaches
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run all analyses for the final board
#24
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jvanheld
closed
2 months ago
jvanheld
commented
3 months ago
[x] make BOARD=${BOARD} -f makefiles/01_init.mk all_metadata
[x] make BOARD=${BOARD} -f makefiles/01_init.mk fetch_sequences
[x] make BOARD=${BOARD} -f makefiles/01_init.mk fastq2fasta
[x] make BOARD=${BOARD} -f makefiles/03_PBM.mk tsv2fasta
[x] make BOARD=${BOARD} -f makefiles/03_PBM.mk top_bg_seq_all_datasets
[x] make BOARD=${BOARD} -f makefiles/01_init.mk rand_fragments_all_experiments
[x] make BOARD=${BOARD} -f makefiles/01_init.mk tf_vs_others_all_experiments
[x] make BOARD=${BOARD} -f makefiles/02_peak-motifs.mk peakmo_all_experiments EXPERIMENTS='CHS GHTS SMS HTS'
[x] make BOARD=${BOARD} -f makefiles/02_peak-motifs.mk peakmo_diff_all_experiments EXPERIMENTS='CHS GHTS SMS HTS'
[x] make BOARD=${BOARD} -f makefiles/03_PBM.mk peakmo_diff_all_datasets
[x] make BOARD=${BOARD} -f makefiles/04_optimize-matrices.mk omga_all_experiments EXPERIMENTS='CHS GHTS SMS HTS'
[x]
adapt omga targets to analyse PBM data !
[x] make BOARD=${BOARD} -f makefiles/04_optimize-matrices.mk omga_collect_tables