lapa.main
Module Contents
Functions
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CLI interface for lapa polyA cluster calling. |
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CLI interface for lapa tss cluster calling. |
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CLI interface for detecting of linking reads. Linking reads are |
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CLI interface for create GTF file with tss/poly(A) cluster support |
- lapa.main.cli_lapa(alignment, fasta, annotation, chrom_sizes, output_dir, counting_method, min_tail_len=10, min_percent_a=0.9, mapq=10, cluster_extent_cutoff=3, cluster_ratio_cutoff=0.05, cluster_window=25, min_replication_rate=0.95, replication_rolling_size=1000, replication_num_sample=2, replication_min_count=1, non_replicates_read_threhold=10)
CLI interface for lapa polyA cluster calling.
- lapa.main.cli_lapa_tss(alignment, fasta, annotation, chrom_sizes, output_dir, mapq=10, cluster_extent_cutoff=3, cluster_ratio_cutoff=0.05, cluster_window=25, min_replication_rate=0.95, replication_rolling_size=1000, replication_num_sample=2, replication_min_count=1, non_replicates_read_threhold=10)
CLI interface for lapa tss cluster calling.
- lapa.main.cli_lapa_link_tss_to_tes(alignment, lapa_dir, lapa_tss_dir, output, mapq=10, min_read_length=100, dataset='all')
CLI interface for detecting of linking reads. Linking reads are the reads start in a tss cluster and in poly(A) cluster. Linking reads represents transcript complete isoforms.
- lapa.main.cli_lapa_correct_talon(links, read_annot, gtf_input, gtf_output, abundance_input, abundance_output, keep_unsupported=False)
CLI interface for create GTF file with tss/poly(A) cluster support based on the linking reads and using splice chain of TALON.