Not detected and unknown alleles

[rahimrajwani]

I have question, about Not detected and unknown alleles number.
How can I analyze our genome with these two word ( for example if i want design phylogenetic tree I can not because i need number in the output table).

Originally posted by @jamalsaad1 in #1 (comment)

[rahimrajwani]

Hi Jamal,

If you really have to use it for the phylogenetic inference, you may consider one of the following:

1. Exclude loci with not detected or unknown allele number from your analysis. For example, if 2 out of 24 loci are either unknown or not detected, you may exclude these 2 loci from your entire dataset and proceed for phylogenetic reconstruction using 22 loci .

2. If the program you are using for phylogenetic inference strictly requires a 24 digit pattern, you may choose to mark an uninformative allele for all samples in your dataset. For example, mark an allele 1 at the not detected locus for all samples in your dataset.

Generally speaking, the problem of not detected or unknown allele number would remain because of the limitations of current sequencing technologies. The program helps you to extract allele numbers for most loci that can be inferred more confidently.

[jamalsaad1]

Thank you for your quick reply Best regard Jamal SAAD PhD student, Aix-Marseille University URMITE,FRANCE Tel: 0658997312 Le lun. 29 oct. 2018 à 07:24, rahimrajwani <notifications@github.com> a écrit :

…

Hi Jamal, If you really have to use it for the phylogenetic inference, you may consider one of the following: 1. Exclude loci with not detected or unknown allele number from your analysis. For example, if 2 out of 24 loci are either unknown or not detected, you may exclude these 2 loci from your entire dataset and proceed for phylogenetic reconstruction using 22 loci . 2. If the program you are using for phylogenetic inference strictly requires a 24 digit pattern, you may choose to mark an uninformative allele for all samples in your dataset. For example, mark an allele 1 at the not detected locus for all samples in your dataset. Generally speaking, the problem of not detected or unknown allele number would remain because of the limitations of current sequencing technologies. The program helps you to extract allele numbers for most loci that can be inferred more confidently. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AlOdoTkLYB6_JCLiwkcIWGd7sgRy5iszks5upp8YgaJpZM4X-Ud5> .