How to use this with two parent and two bulk?

[haohui123]

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]

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? —You are receiving this because you are subscribed to this thread.Reply to this email directly, view it on GitHub, or unsubscribe. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "#18", "url": "#18", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[haohui123]

Thanks you！

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------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "YuSugihara/QTL-seq" <notifications@github.com&gt;; 发送时间:&nbsp;2021年2月22日(星期一) 上午9:30 收件人:&nbsp;"YuSugihara/QTL-seq"<QTL-seq@noreply.github.com&gt;; 抄送:&nbsp;"杨好慧"<475889337@qq.com&gt;;"Author"<author@noreply.github.com&gt;; 主题:&nbsp;Re: [YuSugihara/QTL-seq] How to use this with two parent and two bulk? (#18) 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? —You are receiving this because you are subscribed to this thread.Reply to this email directly, view it on GitHub, or unsubscribe. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "#18", "url": "#18", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ] — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[YuSugihara]

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]

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]

I do NOT recommend, but you can try.

[xiekunwhy]

Hi,

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

[harish0201]

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!