In the line with > if the strand=+ then everything is good except that the calculated range=chr2:166170446-166170451 is 1 digit off. An example is
is
Does the sequence starts at 0 or does it start at 1?
Could you post the sequence that produces that result?
Quote:
Originally Posted by cmccabe
is
[...]
I suppose I am not understanding. I cannot see how the above example AAAAAA or aaaaaa can be a match on the sequence catacgactttcttttttcaaacagGATATCATTATTTCCTGGAGGGTTT
TTTAGATGCACTACTATGTGGAAATAGCTCTGATGCAGGgtaagtcaata
atttgtgtgtatct
Does the sequence starts at 0 or does it start at 1?
Could you post the sequence that produces that result?
1-based coordinate system where the t in green is 166168510 and the t in blue is 166168623. For a sequence that has strand=+ in the > line, the above will always be true and as you move to the right in the sequence the numbers increase from left to right as in the example below.
input
current output
output with correct coordinates (the first T in the repeat is 35 away and there are 5 more repeat T in the sequence).
If in the line with >strand=-, then the last t in greenis 166905371 and the first c in blue is 166905484, the same 1-based coordinate system is applied, but the opposite orientation is true for strand=- and a compliment rule is applied and the numbers decrease from left to right as in the example.
input
Compliment rules
Since the first 6t in the repeat is at 166905472 and there are 5 more t after 166905467. The first coordinate (166905472), is the end, and the last coordinate (166905467) is the start. To further complicate things since the stand=- the 6t is really 6a following the Compliment rules.
Since the next 6T in the repeat is at 166905437 and there are 5 more t after 166905432. The first coordinate (166905437), is the end, and the last coordinate (166905432) is the start. To further complicate things since the stand=- the 6t is really 6A following the Compliment rules.
desired output
The strand=- is a different process and unfortunately the rules that it uses only make it trickier.
I hope this helps and Thank you very much, I really appreciate all your help .
Last edited by cmccabe; 08-22-2018 at 11:15 AM..
Reason: added second question repose with example and description, added details
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