Basenji

Introduction

Basenji is a tool for sequential regulatory activity predictions with deep convolutional neural networks.

For more information, please check its website: https://biocontainers.pro/tools/basenji and its home page on Github.

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