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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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How to use this with two parent and two bulk? #18

Closed haohui123 closed 3 years ago

haohui123 commented 3 years ago

How to use this with two parent and two bulk? Thanks you for your code supply for us! The guide tell us just use a single whole-genome resequencing of either of the parental cultivars. if so, whether the accury of result maybe lower than use two parent?
If use two parents, how can I use your code?

hannyxie commented 3 years ago

you can filtered before input，or just use one parent，in most case one/two parents will get similar result.Or use other pipeline. 

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    On 02/22/2021 09:17, haohui123 wrote:

How to use this with two parent and two bulk? Thanks you for your code supply for us! The guide tell us just use a single whole-genome resequencing of either of the parental cultivars. if so, whether the accury of result maybe lower than use two parent? If use two parents, how can I use your code?

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haohui123 commented 3 years ago

Thanks you！

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you can filtered before input，or just use one parent，in most case one/two parents will get similar result.Or use other pipeline. 

                             解涵

                                 邮箱：18326667320@163.com

     On 02/22/2021 09:17, haohui123 wrote:

How to use this with two parent and two bulk? Thanks you for your code supply for us! The guide tell us just use a single whole-genome resequencing of either of the parental cultivars. if so, whether the accury of result maybe lower than use two parent? If use two parents, how can I use your code?

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YuSugihara commented 3 years ago

Basically, the results should be same in both parental cultivar. However, maybe SNPs which can be used will be different if the input parental cultivar has many missing than another one. If you want to consider the sequences of both parental cultivars, you can run QTL-seq twice.

gplee85 commented 3 years ago

Basically, the results should be same in both parental cultivar. However, maybe SNPs which can be used will be different if the input parental cultivar has many missing than another one. If you want to consider the sequences of both parental cultivars, you can run QTL-seq twice.

Can I input a F1 cultivar for the parental cultivar, or merged bam of P1 and P2 instead of using either one?

YuSugihara commented 3 years ago

I do NOT recommend, but you can try.

xiekunwhy commented 3 years ago

Hi,

You can try https://github.com/xiekunwhy/bsa Best, Kun

harish0201 commented 2 years ago

If you want to consider the sequences of both parental cultivars, you can run QTL-seq twice.

Do you mean run this once with one parent and then run with another? How do we pick the variants then in case there is difference?

Any suggestions would be appreciated!