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Old 11-10-2010, 06:36 PM   #1
mrfox
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Default A few questions on Tophat

Hi everyone,
This is my first post. :-) I am a fresh user of Tophat and here I would like to ask you guys a few questions which confuse me a lot.
I run Tophat 1.0.13 on my Illumina RNA-Seq data (75nt paired end, fly samples). I actually run Tophat without the option -g1 (called run1 below) and with -g1(called run2) respectively. I suppose that the uniquely mapped reads from run1 is the same set from run2. Thus I extract the mapped reads with the field "NH:i:1" from run1 and compared them with all the mapped reads from run2. However, I found that there are a lot more such reads in run1 that does not appear run2. So my question is:
1) If I do not use "-g1", then how can I identify uniquely mapped reads? I guess my understanding that "NH:i:1" means "uniquely mapped" might not be correct.
2)Then I run Tophat on 4 mouse samples, without or with "-g1". This time, I found that for two of the samples, in "accept_hits.sam", I did not find the field "NH", while I did find this field in another two.

Hope I have addressed the questions clearly. Thank you all.:-)
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Old 11-10-2010, 06:41 PM   #2
mrfox
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And in 2), my question is: how can I know when and which these optional fields will be contained in accpet_hits.sam? Thank you.
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