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Old 06-19-2011, 02:34 AM   #1
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Location: Germany

Join Date: Feb 2011
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Default tophat -j junctions option


I have paired end reads and single end reads of the same length. However from tophat manual I found that its better to run tophat first on the paired end read and then obtain the junction file. For the single end read, I could then supply this junction file with the -j parameter.

My question is this: Now I have two junction files, one from the paired end and other from the single end reads (which was obtained by passing the -j parameter). Now, does this mean that I have to merge these two files to obtain all junctions? or just the last junction file gives all possible junctions??

Thank you!
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