Tophat and cufflinks mate-inner-dist option

combiochem · 04-22-2010, 04:16 PM

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 · 04-22-2010, 05:37 PM

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.

Quote:

Originally Posted by 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"?

combiochem · 04-22-2010, 06:02 PM

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

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04-22-2010, 04:16 PM	#1
combiochem Member Location: Los Angeles Join Date: Jul 2009 Posts: 11	Tophat and cufflinks mate-inner-dist option 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"?

04-22-2010, 06:02 PM	#3
combiochem Member Location: Los Angeles Join Date: Jul 2009 Posts: 11	Thanks for the comments and the the other post. It helps.