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wtsi-hpag / Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
MIT License
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pre n50 = scaff10x n50 #19

Open luiscunhamx opened 3 years ago

luiscunhamx commented 3 years ago

Hi,

I hope you can help me out with the following. I am running scaff10x on a pacbio draft assembly and there is no change in metrics after running the software using default parameters. The pipeline runs smoothly and produces all the expected files, but I am, wondering that my 10x data might not be of the best quality after looking at the barcode length distributions and coverage stats in the generated plot. In any case, I would love to get some benefit out of it. So, my question is, can I re-run the pipeline with tweaked parameters using the output files generated in the first run? If yes, what would be the flag for using the align.dat but with different block and edge parameters?

Thanking in advance and waiting for your answer

Luis

mlcossette9224 commented 3 years ago

Hi Luis,

I am having the same issue, did you end up figure out what was wrong?

Marie