Jigme Dorji

7 Questions 10 Answers 0 Followers

Questions related from Jigme Dorji

Which allele (Ref or Alt) is to be considered in heteroplasmic positions while converting alleles in variant positions (vcf) to fasta like sequence?

I have a vcf of mitochondrial chromosome. I am interested to generate a sequence (fasta like ) for the variant positions. It has been pretty straight forward for positions with homoplasmic (GT...

14 November 2019 4,413 1 View

How do we determine if FST is significantly different from zero?

3 horse breeds, 25 animals for each breed, genotyped using 29 microsatellite markers. I have calculated the F-Statistics using F-STAT. The FST value is 0.006. How to test if this value is...

07 February 2018 589 6 View

Any method to impute bovine LD to HD (X and Mitochondrial part)?

Are mitochondrial DNA and X chromosome parts in Bovine LD imputed to either HD/WGS in routine imputation process. If not why and are there any approaches to carry out their imputation. Thanks.

05 October 2017 6,019 0 View

How do you choose a dye to label a primer for fragment analysis using a sequencer?

A primer is labelled with dye; for example FAM, VIC, NED etc for fragment analysis using a sequencer. We see that different primers are labelled with different dyes. Is there any basis to choose a...

15 May 2017 3,963 6 View

Is it a standard to consider NUMTs in PCR amplification for mitochondrial DNA analysis?

We have sequenced D Loop region of Mitochondrial DNA of three types of horses in Bhutan. However, we happened to have overlooked the Nuclear mitochondrial DNA segments (NUMTs) during the...

31 March 2017 6,366 5 View

Can sequences of D-Loop mitochondrial DNA from various individuals in a species using different primers used for phylogentic studies?

There are different primers used in sequencing of D Loop region of mitochondrial DNA in horse. Will different primers not result in different sequences? and Can the sequences obtained using...

30 March 2017 6,282 6 View

How can we make deconjested rootless NJ tree and make the taxon readable in MEGA 7?

I have constructed Neighbor- Joinning tree using mtDNA D-loop sequences from 92 horses using MEGA 7. The dendrogram obtained is so conjested and the sequences unreadable. How do I make the...

01 January 1970 1,001 2 View