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Old 10-15-2010, 08:38 PM   #1
Location: Ames, IA

Join Date: Nov 2008
Posts: 57
Default Tophat options to report unaligned reads and controlling Bowtie options

I run Tophat from command line on our shared Linux environment queue. The gist is this:

$ ~/tophat -o ./tophat_out_s1 -p 4 --solexa1.3-quals ./genome_bwtind/<AGPv1_genome_ind> s_1_sequence.txt
I supply the options -o (for output file) -p (no. of threads) and --solexa1.3-quals (specifying quality). I also specify the path to the bowtie index and finally the actual sequence.txt (fastq) file.

I understand that Tophat runs Bowtie twice. Can I supply an option to Tophat to only report the unaligned reads after its run? I mean something like the bowtie --un option. Similarly on these lines is it possible to control Bowtie paramters from the Tophat command?


Last edited by Siva; 10-15-2010 at 11:15 PM. Reason: Clarity
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