Get statistics on alignments from bam file or
the source of alignment bam files, one of:
alignmentStats queries the bam index files similar
to 'idxstats' from samtools. Please note that this does not
discriminate for example between primary and secondary alignments. If
you need more statistics, see for example
quickBamFlagSummary from package
x is a
qProject object, the auxiliary bam files will
not contain any unmapped reads, and the corresponding unmapped counts
are calculated by subtracting auxiliary mapped counts from the total
reads. The latter correspond to the unmapped counts from the
corresponding genome bam files.
matrix with one row per bam file and three columns
("seqlength", "mapped" and "unmapped").
Anita Lerch, Dimos Gaidatzis and Michael Stadler
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