bam_stat.py

This program is used to calculate reads mapping statistics from provided BAM file. This script determines "uniquely mapped reads" from mapping quality, which quality the probability that a read is misplaced (Do NOT confused with sequence quality, sequence quality measures the probability that a base-calling was wrong) .

Inputs

Input BAM/SAM file: Alignment file in BAM/SAM format.
Minimum mapping quality: Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)

Output

Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
Uniquely mapped Reads = {Splice reads} + {Non-splice reads}

About RSeQC

The RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.

The RSeQC package is licensed under the GNU GPL v3 license.