Hi All,
Sorry but I couldn't find the answer to this question anywhere!
In both cufflinks and cuffdiff, you have the option of specifying -u (multi-read correction) and -b (fragment bias correction). Does anyone know whether these options need to be specified in the command for both programs (in succession) to work properly, or just one or the other?
Also, if anyone has any idea whether/how specifying them once/twice/in the different programs will affect the results, that would be much appreciated too!
Thanks! Kat
Sorry but I couldn't find the answer to this question anywhere!
In both cufflinks and cuffdiff, you have the option of specifying -u (multi-read correction) and -b (fragment bias correction). Does anyone know whether these options need to be specified in the command for both programs (in succession) to work properly, or just one or the other?
Also, if anyone has any idea whether/how specifying them once/twice/in the different programs will affect the results, that would be much appreciated too!
Thanks! Kat