- Try the following accessor methods:
length(aln_chr4)
head(names(aln_chr4))
seqnames(aln_chr4)
strand(aln_chr4)
first(aln_chr4)
last(aln_chr4)
head(start(first(aln_chr4)))
- How many reads are properly paired?
table(isProperPair(aln_chr4))
-
What is the percentage of reads that map to multiple locations?
t=table(names(aln_chr4)) head(t[t>1]) length(t[t>1])/length(t)*100 # let us inspect one of the multireads aln_chr4[names(aln_chr4)=="SRR031714.1029411"] -
What information does the command
seqlevels(aln_chr4)provide?It contains information on the chromosome names available in the BAM file.