Hi there,

I am trying to use IRanges v2.18.3 library in my analysis for the same GTF file for two different alignment files. Though the proper work done for one alignment files, for another one I could see the following lines whcih I am unable to understand.

In range 1: 'end' must be >= 'start' - 1.: .Call2(\"solve_user_SEW0\", start, end, width, PACKAGE = \"IRanges\")"

Please check and let me know if I could provide any other information to rectify the problem.

Thanks, Nagesh

There are a couple of parts to this error message. The important one for you is the first part:

In range 1: 'end' must be >= 'start' - 1.

Which says, at risk of being completely redundant, that in the first range, the end value must be greater or equal to the start value minus one. As an example:

> IRanges(5, 5:3)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  In range 3: 'end' must be >= 'start' - 1.

Which tells us that the third range (with a start of 5 and an end of 3) doesn't fulfill that criterion, but the other two ranges do. Given that a GTF file is text, you could look at the head of the file to see what the problem is.