Tophat : Read Length Warning
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8.9 years ago
narges ▴ 180

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.

tophat • 4.3k views
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reduce your --segment-length to 18

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

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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.

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thank you for your help

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Nicobxl, I would suggest to add this an answer.

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8.9 years ago

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.

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