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I tried to find the junctions for my fastq reads (single end reads, 42 bps). The segment_juncs provided me with 50lakhs possible junctions when trying to find in the whole genome. When I tried to align the same reads with a single chromosome as reference, I still got 5000000 possible junctions. Please explain why does it always give 5000000 outputs? Is there any possible way to reduce the no.of outputs?
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Last edited by iglab; 04-18-2013, 10:50 AM. -
For anyone (like me) who has no idea what a 'lakh' might be it is 100,000 (I googled so you don't have to).
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