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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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Query on the parent sequence input #13

Closed gokulan-15 closed 3 years ago

gokulan-15 commented 3 years ago

Hi, @YuSugihara!

I would like to be clarified on which sequence to input for the --parent option in QTL-seq - Is it the parent that shows the desired phenotype or the one that does not?

Similarly, what should be the input for --cultivar in MutMap: wildtype or the mutant sequence? Your reply to these would be of great help.

Best! Gokulan.

YuSugihara commented 3 years ago

In detail, please look at the original QTL-seq papaer by Takagi et al. (2013).

'--parent' option in QTL-seq is to input a sequence file for either of the parents used to create bulked populations. '--cultivar' option in MutMap is to input a sequence file for NOT mutagenized parent to create bulked populations.

These options are used to polarize the bulked alleles.

gokulan-15 commented 3 years ago

Thanks for the clarification, @YuSugihara!