3. map_stat.py¶

3.1. Description¶

Report reads mapping statistics

Options:

`--version`	show program’s version number and exit
`-h, --help`	show this help message and exit
`-i BAM_FILE, --infile=BAM_FILE`
	Input file in BAM foramt. Must have BAM alignment tags indicated below.
`--cb-tag=CB_TAG`
	BAM alignment tag. Used to indicate error-corrected cellular barcode. default=’CB’
`--re-tag=RE_TAG`
	BAM alignment tag. Used to indicate the region type of the alignment (E = exonic, N = intronic, I = intergenic). default=’RE’
`--tx-tag=TX_TAG`
	BAM alignment tag. Used to indicate reads aligned to the same strand as the annotated transcripts. default=’TX’
`--an-tag=AN_TAG`
	BAM alignment tag. Used to indicate reads aligned to the antisense strand of the annotated transcripts. default=’AN’
`--umi-tag=UMI_TAG`
	BAM alignment tag. Used to indicat the error-corrected UMI. default=’UB’
`--xf-tag=XF_TAG`
	BAM alignment tag. Used to indicate reads confidently mapped to the feature. default=’xf’
`--chrM-id=MIT_CONTIG_NAME`
	The name of mitochondrial chromosome in BAM file. default=’chrM’
`--verbose`	Logical to determine if detailed running information is printed to screen.

3.2. Example¶

$ python3 map_stat2.py -i normal_possorted_genome_bam.bam

2020-10-08 10:06:41 [INFO]  Reading BAM file "normal_possorted_genome_bam.bam" ...
2020-10-08 10:06:41 [INFO]  Processing "chr1" ...
2020-10-08 10:11:50 [INFO]  Processed 24729033 alignments mapped to: "chr1"
2020-10-08 10:12:16 [INFO]  Processing "chr10" ...
2020-10-08 10:17:57 [INFO]  Processed 26004376 alignments mapped to: "chr10"
2020-10-08 10:18:27 [INFO]  Processing "chr11" ...
2020-10-08 10:26:59 [INFO]  Processed 37558210 alignments mapped to: "chr11"
...
...

Total_alignments: 589060389
└--Confident_alignments: 443330914

Total_mapped_reads:     589060389
|--Non_confidently_mapped_reads:        145729475       (24.74%)
└--Confidently_mapped_reads:    443330914       (75.26%)
   |--Reads_with_PCR_duplicates:        327447641       (73.86%)
   └--Reads_no_PCR_duplicates:  115883273       (26.14%)

   |--Reads_map_to_forward(Waston)_strand:      259474203       (58.53%)
   └--Reads_map_to_Reverse(Crick)_strand:       183856711       (41.47%)

   |--Reads_map_to_sense_strand:        443330914       (100.00%)
   └--Reads_map_to_antisense_strand:    0       (0.00%)
   └--Other:    0       (0.00%)

   |--Reads_map_to_exons:       443330914       (100.00%)
   └--Reads_map_to_introns:     0       (0.00%)
   └--Reads_map_to_intergenic:  0       (0.00%)
   └--Other:    0       (0.00%)

   |--Reads_with_Error-Corrected_barcode:       437707874       (98.73%)
   └--Reads_no_Error-Corrected_barcode: 5623040 (1.27%)

   |--Reads_with_Error-Corrected_UMI:   443184634       (99.97%)
   └--Reads_no_Error-Corrected_UMI:     146280  (0.03%)

   |--Reads_map_to_mitochonrial_genome: 56744099        (12.80%)
   └--Reads_map_to_nuclear_genome:      386586815       (87.20%)

   |--Map_consecutively:        242755968       (54.76%)
   |--Map_with_clipping:        49473035        (11.16%)
   |--Map_with_splicing:        115086767       (25.96%)
   |--Map_with_splicing_and_clipping:   19346122        (4.36%)
   └--Others:   16669022        (3.76%)

Note

Except the header section, each row in a BAM file represents an alignment. One read can have multiple alignments.