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Hi! Thanks for this great tool.
I mapped the Nanopore raw reads to CHM13 and found many primary alignment reads have very long soft/hard clipping bases in the outputs. To my understanding, clipped bases are those can't be mapped to the reference. It would be acceptable if the clipped bases are within 100 bases but it really perplexes to have so much difference between the reads and the reference.
grep 'tp:A:P' chm13raw.sam | awk '{print $6}' | grep --color '[HS]'
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