If, instead, the protocol is strand-specific, then the first set of integers in a pair would be applied to fragments where read 1 precedes read 2, and the second set to cases where read 2 precedes read 1. In this case, the first value in each pair is applied to the end of read 1 and the second to the end of read 2. Take the following command as an example:
Given that, the -5 3 set would produce the following::
----> read 1
read 2 <----
------------------------ fragment
-------------------------------- shifted fragment
and the -1 4 set would produce the following::
----> read 2
read 1 <----
------------------------ fragment
--------------------- shifted fragment
As can be seen, such fragments are considered to be on the - strand, so negative values then shift to the left on its frame of reference (thus, to the right relative to the + strand).
The diagram for -1 4 seems to be wrong. Because -1 and 4 has opposite sign, the shift of read 1 and read 2 should also in the opposite directions (see the shift for -5 3).
If, instead, the protocol is strand-specific, then the first set of integers in a pair would be applied to fragments where read 1 precedes read 2, and the second set to cases where read 2 precedes read 1. In this case, the first value in each pair is applied to the end of read 1 and the second to the end of read 2. Take the following command as an example:
.. code:: bash
Given that, the
-5 3set would produce the following::and the
-1 4set would produce the following::As can be seen, such fragments are considered to be on the
-strand, so negative values then shift to the left on its frame of reference (thus, to the right relative to the+strand).The diagram for
-1 4seems to be wrong. Because -1 and 4 has opposite sign, the shift of read 1 and read 2 should also in the opposite directions (see the shift for-5 3).