Dear Minnow authors,
Is there a way to run minnow estimate or change the countProb.txt / geneLevelProb.txt files in a way so that the simulated reads won't have multi-mapping at all? I realize that simulating multi-mapping is a core part of the Minnow algorithm, and that there exists some level of multi-mapping in real data. The tools I'm testing may not deal with multi-mapping well enough, and I'm also trying to compare their performance irrespective of this issue. Would it be possible to get a set of reads where individual reads won't multi-map to different genes? Thank you.
Dear Minnow authors,
Is there a way to run minnow estimate or change the countProb.txt / geneLevelProb.txt files in a way so that the simulated reads won't have multi-mapping at all? I realize that simulating multi-mapping is a core part of the Minnow algorithm, and that there exists some level of multi-mapping in real data. The tools I'm testing may not deal with multi-mapping well enough, and I'm also trying to compare their performance irrespective of this issue. Would it be possible to get a set of reads where individual reads won't multi-map to different genes? Thank you.