Basenji
Introduction
Basenji
is a tool for sequential regulatory activity predictions with deep convolutional neural networks.
Versions
0.5.1
Commands
akita_data.py
akita_data_read.py
akita_data_write.py
akita_predict.py
akita_sat_plot.py
akita_sat_vcf.py
akita_scd.py
akita_scd_multi.py
akita_test.py
akita_train.py
bam_cov.py
basenji_annot_chr.py
basenji_bench_classify.py
basenji_bench_gtex.py
basenji_bench_gtex_cmp.py
basenji_bench_phylop.py
basenji_bench_phylop_folds.py
basenji_cmp.py
basenji_data.py
basenji_data2.py
basenji_data_align.py
basenji_data_gene.py
basenji_data_hic_read.py
basenji_data_hic_write.py
basenji_data_read.py
basenji_data_write.py
basenji_fetch_app.py
basenji_fetch_app1.py
basenji_fetch_app2.py
basenji_fetch_norm.py
basenji_fetch_vcf.py
basenji_gtex_folds.py
basenji_hdf5_genes.py
basenji_hidden.py
basenji_map.py
basenji_map_genes.py
basenji_map_seqs.py
basenji_motifs.py
basenji_motifs_denovo.py
basenji_norm_h5.py
basenji_predict.py
basenji_predict_bed.py
basenji_predict_bed_multi.py
basenji_sad.py
basenji_sad_multi.py
basenji_sad_norm.py
basenji_sad_ref.py
basenji_sad_ref_multi.py
basenji_sad_table.py
basenji_sat_bed.py
basenji_sat_bed_multi.py
basenji_sat_folds.py
basenji_sat_plot.py
basenji_sat_plot2.py
basenji_sat_vcf.py
basenji_sed.py
basenji_sed_multi.py
basenji_sedg.py
basenji_test.py
basenji_test_folds.py
basenji_test_genes.py
basenji_test_reps.py
basenji_test_specificity.py
basenji_train.py
basenji_train1.py
basenji_train2.py
basenji_train_folds.py
basenji_train_hic.py
basenji_train_reps.py
save_model.py
sonnet_predict_bed.py
sonnet_sad.py
sonnet_sad_multi.py
sonnet_sat_bed.py
sonnet_sat_vcf.py
tfr_bw.py
tfr_hdf5.py
tfr_qc.py
upgrade_tf1.py
Module
You can load the modules by:
module load biocontainers
module load basenji
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run Basenji on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=basenji
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers basenji