Announcement

Collapse
No announcement yet.

General question about TopHat

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • General question about TopHat

    I am using TopHat for some analyses. The program requires the expected mean of the inner distances of the paired reads as a parameter.

    However, why does the program need the expected mean inner distance? How does it use this information?

    I could not find this information in the online manual.

    Thanks.

  • #2
    I think it uses it for flagging reads as "properly paired" in the output BAM/SAM file. There may be other ways it uses it but I don't know about those.

    Comment

    Working...
    X