How do I find the expected (mean) inner distance between mate pair?
I am having an issue with tophat and I think it is because I have 150bp paired end data and I didn't change the -r argument for tophat.
tophat -r ???? ref_genome file-1.fastq file-2.fastq
I've been looking at this post:
I have my QC report, but I am not sure what I am looking at.