What Does The Genome-Read-Mismatches Option Do Intophat

Question

[Varun Gupta]

Hii Everyone

I am using tophat2 software for mapping reads. In the Advanced Options section for tophat2 i come across 2 options namely

 --genome-read-mismatches       <int>       [ default: 2 ]
 -N/--read-mismatches           <int>       [ default: 2  ]

Can someone explain me what is the difference between these options.

Hope to hear from you guys..

Regards

Answer 1

[Istvan Albert]

This has been answered in Understanding --genome-read-mismatches and --read-mismatches parameter in tophat