Entering edit mode
3.3 years ago
Min Heo
•
0
How to get sequence combination with Rsamtsools? (Input: Bamfile)
Like this:
seqnames pattern count range
chr1 ATTCG 1 chr1:3222724-3222729
chr1 ATTAG 2 chr1:3222724-3222729
chr1 ACTAG 2 chr1:3222724-3222729
Your question is a little too brief to understand. A BAM file has alignment positions, what is it you mean by "combination"? And what are you counting? You can use rtracklayer, or GenomicAlignments to import a BAM file, and the result will be seqnames and ranges for each read, in an object of your choice (e.g. GenomicRanges). Can you explain more about what your are trying to do with your BAM file?