Tophat : Read Length Warning

Question

[narges]

Hello, I am running tophat over reads with length equal to 36 to 38. And while running it the below warning appears when checking the run:

Warning: you have only one segment per read. If the read length is greater than or equal to 45bp, we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segment

should I make any changes to the process? Thanks a lot.

[Nicolas Rosewick]

reduce your --segment-length to 18

[narges]

Thank you And do not you believe this length is too short to get meaningful result? or this is however the only solution?

[Nicolas Rosewick]

To use tophat for splice read mapping, that's the only solution. tophat first try to align the whole reads. After that it cut the unmapped reads in little segment ( here in your case in 18nt long segment) and try to map it again.

[narges]

thank you for your help

[Sukhi Singh]

Nicobxl, I would suggest to add this an answer.

Answer 1

[Nicolas Rosewick]

reduce your --segment-length to 18. To use tophat for splice read mapping, that's the only solution. tophat first try to align the whole reads. After that it cut the unmapped reads in little segment ( here in your case in 18nt long segment) and try to map it again.