checkSequenceNames | R Documentation |
The MitoTrace function calculates mitochondrial heteroplasmies in (single-cell) RNA sequencing data based on the reads pileups of the mitochondrial genome.
MitoTrace(bam_list = bams, ref_fasta = fasta_loc, name = "MT", max_depth = "",
min_base_quality = "", min_mapq = "", min_nucleotide_depth = "", min_minor_allele_depth = "")
bams_list |
Vector of absolute path(s) pointing to BAM alignment file(s). |
ref_fasta |
Absolute path to the mitochondrial reference genome in FASTA format. |
name |
Name of mitochondrial genome as specified in the BAM files. Sequence names can be check with the checkSequenceNames() function. |
tag_name |
The name of the tag corresponding the cellular barcode. Default = "CB". For droplet scRNAseq only. |
min_read |
The minimum number of read counts to be considered a valid barcode (cell) in the analysis. Default = 1000. For droplet scRNAseq technologies only. |
max_depth |
The maximum depth of reads considered at any position. |
min_base_quality |
The minimum read base quality below which the base is ignored when summarizing pileup information. |
min_mapq |
The minimum mapping quality below which the entire reads is ignored. |
min_nucleotide_depth |
integer(1); minimum count of each nucleotide at a given position required for said nucleotide to appear in the result. |
min_minor_allele_depth |
integer(1); minimum count of all nucleotides other than the major allele at agiven position. |
result <- MitoTrace(bam_list = bams, ref_fasta = fasta_loc, chr_name = "MT", max_depth = "1e6", min_base_quality=25, min_mapq=30, min_nucleotide_depth=0, min_minor_allele_depth=0)
See packageDescription("MitoTrace") for more details.
Read counts matrix and coverage matrix.
This package could not only apply for the analysis of single-cell data but also for bulk seuqencing data.
Mingqiang WANG <Mingqiang.Wang@uth.tmc.edu>, Simon Lukas <lkmklsmn@gmail.com>
The current source code of MitoTrace is from https://github.com/lkmklsmn/MitoTrace.
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