lapa.link
Module Contents
Functions
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Read read_name and locus of reads from alignment file. |
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Link reads to transcript end sites |
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Link reads to transcript start sites |
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Link transcript site sites to transcript end sites using |
Attributes
- lapa.link._reads_cols = ['read_name', 'Chromosome', 'read_Start', 'read_End', 'Strand']
- lapa.link._read_alignment_reads(alignment, mapq=10, min_read_length=100)
Read read_name and locus of reads from alignment file.
- lapa.link._link_reads_to_tes(df_tes_cluster, df_reads, distance=50)
Link reads to transcript end sites
- lapa.link._link_reads_to_tss(df_tss_cluster, df_reads, distance=50)
Link reads to transcript start sites
- lapa.link.link_tss_to_tes(alignment, lapa_dir, lapa_tss_dir, distance=50, mapq=10, min_read_length=100, dataset='all')
Link transcript site sites to transcript end sites using long-read from the alignment file.
- Parameters
alignment (str) – Path to bam file or TALON read_annot file.
lapa_dir (str) – Path to lapa output directory generated with lapa command
lapa_tss_dir (str) – Path to lapa tss directory with lapa_tss command