View source: R/plot_fragments.R
get_fragment_length_bed | R Documentation |
This function takes a BAM file and a BED file as an input and outputs the fragment length distributions of all the regions in a TXT file.
get_fragment_length_bed( bin_path = "tools/samtools/samtools", bam = "", bed = "", max_frag_length = 1000, mapq = 10, threads = 1, output_dir = "", verbose = FALSE, mode = 0, start = NULL, end = NULL, start_bin = NULL, end_bin = NULL )
bin_path |
Path to samtools executable. Default path tools/samtools/samtools. |
bam |
Path to BAM file. |
bed |
Path to BED file. |
max_frag_length |
Maximum fragment length to keep. Default 1000. |
mapq |
Minimum MapQ of the reads to keep. Default 10. |
threads |
Number of cores. Default 1 |
output_dir |
Directory to output results. |
verbose |
Enables progress messages. Default False. |
mode |
Mode in which to output the fragment length. Default 0. Mode 0: Returns fragment length for R1 and R2 reads. Mode 1: Returns fragment legnth for R1 reads. Mode 2: Returns fragment length for R2 reads. |
start |
Downstream distance from (start+end)/2 position in bed file |
end |
Upstream distance from (start+end)/2 position in bed file |
start_bin |
Downstream distance from (start+end)/2 position in bed file for bin |
end_bin |
Upstream distance from (start+end)/2 position in bed file for bin |
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