Tophat and cufflinks mate-inner-dist option

[combiochem]

I'd like to run two programs for the paired-end reads.
The question is that if the mate-inner-dist is less than 0, can I put the number which is less that 0?

For example, when the RNA fragment size in the library is around 140bp and the read length is 75bp, theoretically, mate-inner-dist is going to be "-10" (75*2-140).
In this case, do I have to put the "-10" or simply "0"?

[wenhuang]

I had the same question before and it was answered by Cole Trapnell in this thread:

http://seqanswers.com/forums/showthread.php?t=4355

basically you can specify a negative integer. My results tell me that they were correctly mapped.

I'd like to run two programs for the paired-end reads.
The question is that if the mate-inner-dist is less than 0, can I put the number which is less that 0?

For example, when the RNA fragment size in the library is around 140bp and the read length is 75bp, theoretically, mate-inner-dist is going to be "-10" (75*2-140).
In this case, do I have to put the "-10" or simply "0"?

[combiochem]

Thanks for the comments and the the other post. It helps.