**90**wrote:

#### Hi,

I'm confused are these two the same or different values?

I have tun Picard for calculate Mean Insert size of subset of my RNA-seq FASTQ mapped to cDNA (100bp reads) and it gives me:

MEDIAN_INSERT_SIZE 176 MEDIAN_ABSOLUTE_DEVIATION 39 MIN_INSERT_SIZE 12 MAX_INSERT_SIZE 6467 MEAN_INSERT_SIZE 193.140364

So what value should I feed to Tophat - Mean inner distance between mate pairs? 193 or?

And then somewhere I saw which confused me more ---> Mean inner distance between mate pairs = mean insert-size-2*read_length

**15k**• written 2.4 years ago by manekineko •

**90**