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Old 11-18-2010, 05:39 AM   #1
darked89
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Question tophat/cufflinks for novel genome annotation

I got a novel plant genome in an advanced draft phase and 8 Illumina paired RNA-Seq lanes, The RNA-Seq data is mostly from other strains, and the read lengths differ between lanes.
The goal is to get as many "true" genes/transcripts as possible. Hence my questions:

* should I combine all filtered reads into giant 20+GB X_1 and X_2 files and run it with tophat, giving some rough --mate-inner-dist?

* or is it better to run each lane separately with more accurate mate-inner-dist value, then combine it and sort for cufflinks?

* what is the "good practice" to obtain long gene models and keep the number of artifacts low?

* does anybody have a good experience with some alternative to bowtie spliced read mapper, output of which can be used by cufflinks?

BTW, I am using latest tophat (1.1.4), cufflinks etc.
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Old 11-18-2010, 06:53 AM   #2
darked89
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Default

Just found the answer in another thread:

http://seqanswers.com/forums/showpos...5&postcount=27
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