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bbcu.singleCellBamQueries-1.0.4
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مشاهده بیشترتوضیحات
Queries on bam file of single cell per genome position for finding rare mutations
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bbcu.singleCellBamQueries-1.0.4 |
| نام | bbcu.singleCellBamQueries |
| نسخه کتابخانه | 1.0.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Refael Kohen |
| ایمیل نویسنده | refael.kohen@weizmann.ac.il |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/bbcu.singleCellBamQueries/ |
| مجوز | - |
## Queries on bam file of single cell per genome position for finding rare mutations
single-cell-bam-queries.py --help
usage: single-cell-bam-queries.py [-h] --input-file INPUT_FILE --output-file
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]
Queries on bam file of single cell per genome position.
The bam file must be sorted and indexed with the commands:
samtools sort filename.bam > filename.sorted.bam
samtools index filename.sorted.bam
By default the umi and barcode cells are comptible to bam files from cellranger.
For other formats you need to change the parameters of tags and cell barcodes.
Pre-request: python package: pysam
optional arguments:
-h, --help show 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)
نحوه نصب
نصب پکیج whl bbcu.singleCellBamQueries-1.0.4:
pip install bbcu.singleCellBamQueries-1.0.4.whl
نصب پکیج tar.gz bbcu.singleCellBamQueries-1.0.4:
pip install bbcu.singleCellBamQueries-1.0.4.tar.gz