Genetic map

Denis

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Oct 29, 2021, 1:12:19 PM10/29/21

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Hi,

I'd like to construct a genetic map from F2 population data. Now i'm dealing with a very small data set: just a few markers for 300 individuals, but will work with large data sets in the future. This is why i'd prefer to learn qtl2 instead of qtl. I've found detailed tutorial on map construction using qtl package (https://rqtl.org/tutorials/geneticmaps.pdf). I'm wondering where can i find the tutorial on genetic map construction but using qtl2?

Regards,

Denis

Karl Broman

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Oct 29, 2021, 4:14:00 PM10/29/21

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There are few facilities for genetic map construction in R/qtl2, and it's not a particularly high priority for me, so I don't think it's likely to expand much in the future.

karl

Denis

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Oct 29, 2021, 4:44:22 PM10/29/21

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Hi Karl,

Thanks for your reply!

Could you advise me please where may i find an examples of using qtl2 for genetic maps building? Would you recommend to use qtl instead? Does qtl contain more options and hence is more suitable for genetic map construction?

Regards,

Denis

пятница, 29 октября 2021 г. в 23:14:00 UTC+3, kbr...@gmail.com:

Karl Broman

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Oct 29, 2021, 4:47:54 PM10/29/21

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R/qtl2 includes the function est_map() that re-estimates the inter-marker distances for a given marker order.

But none of the other things in R/qtl1 have been implemented.

But for that matter, the functions in R/qtl1, described in the tutorial you mentioned, are pretty primitive and you may want to look for alternative tools.

karl

Denis

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Oct 30, 2021, 10:52:16 AM10/30/21

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Hi Karl,

Thank you so much!

Regards,

Denis

пятница, 29 октября 2021 г. в 23:47:54 UTC+3, kbr...@gmail.com:

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