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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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AN INCORRECT FILE FORMAT! #201

Open wangwenzheng-agis opened 1 year ago

wangwenzheng-agis commented 1 year ago

someone can help me? use it to assemble the cholorplast but it gives me that answer,my fasta file was mapped to the whole genome and get with samtools fastq from the bam file ,is it the reason?

ndierckx commented 1 year ago

Hi,

I doesn't recognize the read ids. But have you tried to just use the complete dataset, almost always the best way to assemble. I would advice not to use reads that are extracted from an alignment..

wangwenzheng-agis commented 1 year ago

Hi， sir I solve the problem by using the complete seq, after that the result contain invalid basic group ‘R’ and ’S’,can you tell me what’s that mean, and should I delete it or in some other ways? wish for you William Wang

2023年3月16日 下午10:47，Nicolas Dierckxsens @.***> 写道：

Hi,

I doesn't recognize the read ids. But have you tried to just use the complete dataset, almost always the best way to assemble. I would advice not to use reads that are extracted from an alignment..

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ndierckx commented 1 year ago

These are ambiguous nucleotide codes, if some software doesn't recognizes them, just replace them by an N