I would like to ask if it is possible to change the seqnames of a bam file
giving a vector of character to the function renameSeqlevels. This is
because in order to use the fuction summarizeOverlap or count/find, the
seqnames have to match.
>From the bamfile below I have extracted the locus annotations form the
seqnames (i.e ERCC00002, NC_001133.9...etc) and I have created a list (same
length as the seqlevels of the bam file).
GAlignments object with 6 alignments and 0 metadata columns: