寻找稀有突变的单细胞基因组位置bam文件查询

bbcu.singleCellBamQueries的Python项目详细描述


##查询每个基因组位置单个细胞的bam文件以查找罕见突变

single-cell-bam-queries.py–帮助

用法:single-cell-bam-queries.py[-h]–输入文件输入文件–输出文件
OUTPUT_FILE [–coordinates COORDINATES] [–filtered-cell-barcodes-file FILTERED_CELL_BARCODES_FILE] [–min-mapq MIN_MAPQ] [–max-gene-length MAX_GENE_LENGTH] [–threads THREADS] [–min-cells MIN_CELLS] [–max-cells MAX_CELLS] [–min-mutated-umis MIN_MUTATED_UMIS] [–max-mutated-umis MAX_MUTATED_UMIS] [–min-reads-per-non-mutated-umi MIN_READS_PER_NON_MUTATED_UMI] [–max-reads-per-non-mutated-umi MAX_READS_PER_NON_MUTATED_UMI] [–min-non-mutated-umis MIN_NON_MUTATED_UMIS] [–max-non-mutated-umis MAX_NON_MUTATED_UMIS] [–min-reads-per-mutated-umi MIN_READS_PER_MUTATED_UMI] [–max-reads-per-mutated-umi MAX_READS_PER_MUTATED_UMI] [–enable-cells-with-invalid-umis-num] [–enable-umis-with-invalid-reads-num] [–tag-of-umi TAG_OF_UMI] [–tag-of-cell-barcode TAG_OF_CELL_BARCODE] [–umi-start UMI_START] [–umi-length UMI_LENGTH] [–cell-barcode-start CELL_BARCODE_START] [–cell-barcode-length CELL_BARCODE_LENGTH] [–log-file LOG_FILE]

对每个基因组位置的单个细胞bam文件的查询。

必须使用以下命令对BAM文件进行排序和索引:

samtools sort filename.bam>;文件名.sorted.bam samtools索引filename.sorted.bam

默认情况下,UMI和条形码单元格与CellRanger中的BAM文件兼容。 对于其他格式,需要更改标记和单元格条码的参数。

预请求:python包:pysam

可选参数:
-h, --helpshow this help message and exit
--input-file INPUT_FILE
Full path to input .bam or .sam file (default: None)
--output-file OUTPUT_FILE
Full path to output file name (default: None)
--coordinates COORDINATES
Coordinates of the genome. The default is all genome. For example: chr1:1000000-2000000, or for all chromosom: chr1 (default: all)
--filtered-cell-barcodes-file FILTERED_CELL_BARCODES_FILE
Text file with list of cell barcodes. Counts only these cells (optional) (default: None)
--min-mapq MIN_MAPQ
Minimum quality of the read mapping (default: 10)
--max-gene-length MAX_GENE_LENGTH
Maximum length of the gene. Reads that will be mapped to longer bases will be discarded (default: 100000)
--threads THREADS
number of threads. You can run the chromosome itself in several threads. You can use this prameter only if you specify the start and end coordinates explicitely in the format: chr1:0-14000000 or if the bam file contains header lines with the lengths of the chromosomes, you can check it with the commands: samtools view -h filename.bam (default: 1)
--min-cells MIN_CELLS
mininum cells in genome position that contains the number of umis and reads according to the other parameters (default: 1)
--max-cells MAX_CELLS
maximum cells in genome position that contains the number of umis and reads according to the other parameters (default: 1000000000)
--min-mutated-umis MIN_MUTATED_UMIS
mininum umis per cell that all reads contain mutation in the position (default: 1)
--max-mutated-umis MAX_MUTATED_UMIS
maximum umis per cell that all reads contain mutation in the position (default: 1000000000)
--min-reads-per-non-mutated-umi MIN_READS_PER_NON_MUTATED_UMI
mininum reads in at least one of umis in the cell in genome position (default: 1)
--max-reads-per-non-mutated-umi MAX_READS_PER_NON_MUTATED_UMI
maximum reads in at least one of umis in the cell in genome position (default: 1000000000)
--min-non-mutated-umis MIN_NON_MUTATED_UMIS
mininum umis per cell that all reads not contain mutation in the genome position (default: 1)
--max-non-mutated-umis MAX_NON_MUTATED_UMIS
maximum umis per cell that all reads not contain mutation in the genome position (default: 1000000000)
--min-reads-per-mutated-umi MIN_READS_PER_MUTATED_UMI
mininum reads in at least one of umis in the cell in genome position (default: 1)
--max-reads-per-mutated-umi MAX_READS_PER_MUTATED_UMI
maximum reads in at least one of umis in the cell in genome position (default: 1000000000)
--enable-cells-with-invalid-umis-num
enable positions that contain cell/s with not valid umis number (according to ther range in the other parameters) (default: False)
--enable-umis-with-invalid-reads-num
enable positions that contain umi/s with not valid reads number (according to ther range in the other parameters) (default: False)
--tag-of-umi TAG_OF_UMI
the tag of umi in bam file (default: UR)
--tag-of-cell-barcode TAG_OF_CELL_BARCODE
the tag of umi in bam file (default: CR)
--umi-start UMI_START
location in tag where the umi start (0-based) (default: 0)
--umi-length UMI_LENGTH
length of umi (default: 10)
--cell-barcode-start CELL_BARCODE_START
location in tag where the cell barcode start (0-based) (default: 0)
--cell-barcode-length CELL_BARCODE_LENGTH
length of cell barcode (default: 16)
--log-file LOG_FILE
Log File (default: None)

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