├── README.md ├── add_corrected_barcode_to_read_name.sh ├── barcard ├── calculate_jaccard_index_cbs.py ├── calculate_jaccard_index_cbs_10x_compare.py └── merge_cbs_over_jaccard_index_threshold.py ├── barcode_10x_scatac_fastqs.sh ├── calculate_saturation_10x_samples.py ├── calculate_saturation_from_fragments.py ├── correct_barcode_from_fastq.seq ├── correct_barcode_from_fastq.sh ├── create_issaac_seq_barcode_fastq_for_star_solo.sh ├── create_scifi_rna_barcode_fastq_for_star_solo.sh ├── extract_and_correct_and_split_scalebio_atac_barcode_from_fastq.sh ├── extract_and_correct_biorad_barcode_from_fastq.seq ├── extract_and_correct_biorad_barcode_from_fastq.sh ├── extract_and_correct_hydrop_atac_barcode_from_fastq.seq ├── extract_and_correct_hydrop_atac_barcode_from_fastq.sh ├── extract_and_correct_hydrop_rna_barcode_from_fastq.seq ├── extract_and_correct_hydrop_rna_barcode_from_fastq.sh ├── extract_and_correct_issaac_seq_barcode_from_fastq.seq ├── extract_and_correct_scalebio_atac_barcode_from_fastq.seq ├── extract_and_correct_scalebio_atac_barcode_from_fastq.sh ├── extract_and_correct_scifi_rna_barcode_from_fastq.seq ├── extract_hydrop_atac_barcode_from_R2_fastq.sh ├── fastq_subset.sh ├── filter_fastq_by_read_names.sh ├── filter_star_solo_raw_count_matrix.py ├── fix_R2_read_10x_scATAC_and_10x_multiome_ATAC_fastq.sh ├── fix_scalebio_atac_fastqs.sh ├── fix_sra_fastq.sh ├── fragments_to_bw.py ├── fragments_to_cut_sites.sh ├── limit_aviti_fastq_to_max_q40.sh ├── mapping_stats.sh ├── mark_or_remove_duplicates_per_barcode.sh ├── run_seq_program.sh ├── rust ├── Cargo.toml └── src │ └── bin │ ├── bam_update_cell_barcode.rs │ ├── create_fragments_file.rs │ ├── create_fragments_file_htslib.rs │ ├── create_parsebio_per_sample_bams.rs │ ├── fastq_count.rs │ ├── split_bams_per_cluster.rs │ └── split_bams_per_cluster_htslib.rs ├── seq_lib ├── barcode_correction.codon ├── barcode_correction.seq ├── utils.codon └── utils.seq ├── split_scalebio_atac_fastqs.sh ├── subset_bam_per_cb.sh └── test └── barcode_10x_scatac_fastqs ├── input_R1.fastq ├── input_R2.fastq ├── input_R2.with_corrected_bc.fastq ├── input_R3.fastq ├── output_interleaved_false_add_barcode_in_comment_false_with_bc_read_name_sep_underscore_R1.fastq.gz ├── output_interleaved_false_add_barcode_in_comment_false_with_bc_read_name_sep_underscore_R2.fastq.gz ├── output_interleaved_false_add_barcode_in_comment_true_R1.fastq.gz ├── output_interleaved_false_add_barcode_in_comment_true_R2.fastq.gz ├── output_interleaved_false_add_barcode_in_comment_true_with_corrected_bc_R1.fastq.gz ├── output_interleaved_false_add_barcode_in_comment_true_with_corrected_bc_R2.fastq.gz ├── output_interleaved_true_add_barcode_in_comment_true_interleaved.fastq.gz └── output_interleaved_true_add_barcode_in_comment_true_with_bc_tag_XX_and_bc_qual_tag_YY_interleaved.fastq.gz /README.md: -------------------------------------------------------------------------------- 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