User: nataliagru1

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nataliagru150
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Posts by nataliagru1

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Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... apologies I meant to add this as a comment not an answer. Can this kindly be deleted as an answer my apologies. ...
written 13 days ago by nataliagru150
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Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... Hi Zev, Thank you for your code. The function plot.admixture is unable to save as a function in the R environment after running the loop. plot.admixture<-function("/Users/grubent/Documents/Admixture/"){ Therefore when I attempt to plot the results or save the results as you describe here: ...
written 13 days ago by nataliagru150
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Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... hello you need to add a backslash to your directory like this: "~/Documents/admixture_macosx-1.23/" ...
written 13 days ago by nataliagru150
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Comment: C: Count total number of Homozygous/Heterozygous SNPs from VCF file
... https://www.realtimegenomics.com/products/rtg-tools ...
written 3 months ago by nataliagru150
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Comment: C: Count total number of Homozygous/Heterozygous SNPs from VCF file
... Thank you for your comment. I also found this tool to summarize SNP data very nicely.[1] https://www.realtimegenomics.com/products/rtg-tools [1]: https://www.realtimegenomics.com/products/rtg-tools ...
written 3 months ago by nataliagru150
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Count total number of Homozygous/Heterozygous SNPs from VCF file
... Dear Community, I would like to count the total number of heterozygous and homozygous SNP's in my VCF file. I have read up on other forums but I can't seem to find an answer/guidance on how to perform this. I am simply wondering if there is a simple way to calculate total heterozygous SNPs and to ...
vcf allele snp written 3 months ago by nataliagru150 • updated 3 months ago by colindaven2.3k
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Comment: C: BLASTn output format start position larger than stop position
... Thank you very much for your response. It seems as though I didn't intuitively read the manual. Its clear to me now! Greatly appreciated ...
written 3 months ago by nataliagru150
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BLASTn output format start position larger than stop position
... Dear Community, I am currently running an experiment to identify gene expansion in parasite genomes. I have collected respected gene sequences and created a blast database of my parasite reference genomes using blast db function. I use blastn and search against my parasite reference genome with m ...
blastn output blast outfmt 6 blast blastn written 3 months ago by nataliagru150 • updated 3 months ago by Sej Modha4.7k
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Comment: C: Remove sequences with (50% gaps) from MSA
... Thank you very kindly for your response!! Very helpful indeed! I had some computer issues and am now re-installing biopython and other programs! Will test your code and report back once I have everything up and running! Greatly appreciate you taking the time! ...
written 3 months ago by nataliagru150
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Comment: C: Remove sequences with (50% gaps) from MSA
... Thank you for your response. Yes, I first did remove columns that had a majority position in gaps with trimAL. It's the later I am having an issue with. I am uncertain of trimAL parameters to remove undesirable sequences and was, therefore, wondering if there was a simple way to write a script to re ...
written 3 months ago by nataliagru150

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