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Old 08-08-2010, 07:31 PM   #1
sanwen
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Default how to set seed length in Tophat

how to set seed length? When i try to run Tophat, it always showed "seed length: 90bp", but my reads are only 90bp, i would like to set the seed length to 35bp, but i fail to find any parameter in Manual.
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Old 08-08-2010, 11:04 PM   #2
nicklin
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Under Advanced options:

--segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
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Old 08-10-2010, 12:07 AM   #3
sanwen
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Quote:
Originally Posted by nicklin View Post
Under Advanced options:

--segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
this option does not change the seed length. I did not set this option, but when i try to run Tophat, it still showed seed length was 90bp.
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