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Hello,
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!
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!