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Minimum Copy Number Issue #10
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It sounds weird to me. |
The plasmid in question has a length of around 15 kb and most of the consensus reads when using -c 2 are around 5 kb. |
Hi, you mentioned that "TideHunter allowed me to set the minimum copy number (-c) to 1 without crashing", however TideHunter was not meant to output any consensus sequence with less than 2 copies (which can not be called as tandem repeat) by default. I am going to set a hard threshold for the minimum copy number: >= 2. |
I have data that the insert is long enough that it isn't guaranteed to repeat twice within a read but could have partial repeats. I used a previous version of TideHunter that allowed me to set the minimum copy number (-c) to 1 without crashing even though the default is 2 and produced consensus data for the long insert. This current version errors when I set -c to 1 ([abpoa_gen_cons] No enough sequences to perform msa.) and fails to produce consensus reads for my longer insert with the default of 2. I was wondering if there was a work around to generating consensus reads for this data with the current version.
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