Tophat paired end parameters

[gokhulkrishnakilaru]

Hello Friends,

I am very new to NGS even though I am studying Bioinformatics.

While trying to gain hands on experience on NGS analysis, I have been using tophat on paired end data. I used the following command and my mentor said that my -r option was wrong and asked me to figure it out. The code ran smoothly and I even got the output. But, wat was my mistake is a major concern now.

So, any help is appreciated.

tophat -r 140 -p 4 -o /path/output/ --solexa1.3-quals --library-type fr-unstranded /path/to/ebwt_files /path/to/s_7_1.fq /path/to/s_7_2.fq

[cedance]

Did you check tophat manual to look for what -r option means?
-r/--mate-inner-dist <int> This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs.

Now, how did you figure out the number 140?