From Genome Analysis Wiki
Jump to navigationJump to search
1,172 bytes removed
, 11:53, 30 April 2012
| Line 33: |
Line 33: |
| | | | |
| | =Handling Overlaps= | | =Handling Overlaps= |
| − | | + | '''Use Clip Overlap instead.''' |
| − | If the -c option is used, SuperDeDuper looks for paired-end reads in which the two ends overlap, as shown below.
| |
| − | | |
| − | Read1: A C T G A A C C T T G G A A A C T G C C
| |
| − | Read2: C T T G G A A A C T G C C G G G G A C T
| |
| − | | |
| − | For each end, the average base quality is found for the bases in the region of overlap. (There may be a different number of bases due to insertions and deletions.) The end with the lower average base quality is then soft clipped in the region of overlap. For example, suppose that the cigars for the two reads above are 20M and that Read1 has a lower average base quality in the overlap. Then the cigar for Read1 will be replaced by 7M13S.
| |
| − | | |
| − | If the -s option is used, this behavior persists with the following actions taken as well. Though one end may have a lower average base quality in the region of overlap, it may have individual bases with a higher quality than their corresponding bases in the other end. In this case, those higher quality bases are swapped into the end with the higher average base quality in the region of overlap. This potentially modifies the sequence, the cigar, and the base quality string for the end with the higher average base quality.
| |
