Hi,
I've been recently using bamToBed utility from the bedtools suite in order to transform the alignments in a BAM file into features of a BED file.
I have one question regarding the way bamToBed handles the "S" operation in the cigar string.
For example, I have this alignment (in BAM/SAM format, obtained using STAR mapper. I'm omitting certain not relevant parts of the alignment):
that bamToBed transforms to the following BED feature:
I was just wondering why the BED feature is 25 nts. long (25M), and starts at the same position of the BAM alignment. Considering that the first operation in the cigar string is 4S, shouldn't the BED feature start 4 nucleotides after the position of the BAM alignment?
Thanks a lot in advance.
I've been recently using bamToBed utility from the bedtools suite in order to transform the alignments in a BAM file into features of a BED file.
I have one question regarding the way bamToBed handles the "S" operation in the cigar string.
For example, I have this alignment (in BAM/SAM format, obtained using STAR mapper. I'm omitting certain not relevant parts of the alignment):
Code:
HANNIBAL_0054_FC62M9BAAXX:7:53:2326:12457#0/1 0 chr1 28166 251 4S25M7S * 0 0 ...
Code:
chr1 28165 28190 HANNIBAL_0054_FC62M9BAAXX:7:53:2326:12457#0/1 251 +
Thanks a lot in advance.
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