I am trying to make a chain file to use in liftOver and these can be made using PSL or AXT files. My current data is in SAM/BAM. What's the best way to convert this to a psl or axt format?
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Perhaps you could try passing the output from the sam2bed script to the bed2psl.py script. I'd take care to make sure coordinate indexing is correct at each step of the process.
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