User: krishnakatyal5121

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Posts by krishnakatyal5121

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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Greetings I have mailed the administrator,If I have caused any incoviniance I ask for apologies. Thanks alot , I request if you could help me with my problem.stay safe ...
written 4 weeks ago by krishnakatyal51210
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... greetings Thanks alot for your valuable suggestion i will make sure to follow the method you have prescribed ...
written 4 weeks ago by krishnakatyal51210
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hola kevin gracias por un tutorial tan maravilloso I have my few sample files and I want to merge them with the 1000 genome and want to perform the PCA. I followed your great tutorial but I get an error at step 4. I am using bcftools 1.3 and I have performed all steps 1,2,3. Here you can see I ha ...
written 5 weeks ago by krishnakatyal51210 • updated 4 weeks ago by _r_am31k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hello ` bcftools norm -m-any --check-ref w -f human_g1k_v37.fasta \ data.vcf | \ bcftools annotate -x ID -I +'%CHROM:%POS:%REF:%ALT' | \ bcftools norm -Ob --rm-dup both \ > data.bcf ; ` result : chrM not found error After removing the chrM the same command ga ...
written 7 months ago by krishnakatyal51210
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hello kevin i used an editor named as em editor to change the vcf file since the annotation in the fasta file and my vcf file was different i changed my vcf file accordingly chr1 became 1 chr 2 became 2 and so on and i removed the chrM from my data, by following this method might have preserved the ...
written 7 months ago by krishnakatyal51210
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hello kevin THANKS A LOT !!! I remove the chroM varians from my data using the `grep -w '^#|^#CHROM|^chr[1-22]' my.vcf > my_new.vcf` (I hope it keeps the header and the 22 chr I need) as other methods were either giving index error or header error. but now I get an error![my error][1] Now I ...
written 7 months ago by krishnakatyal51210 • updated 4 months ago by _r_am31k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hello kevin I am using bcftools to normalize and annotate variants. [link to my data][1] a vcf of 10mb When i try to convert the data in bcf like the third step of this wonderful tutorial. I get an error the sequence chrM not found. The error message indicates that there are some variants on the mit ...
written 7 months ago by krishnakatyal51210
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Thanks alot kevin I dont have any fasta file just a vcf (freebayes) and i want to perform pca to check out similarity of my sample with other ethnic groups do i need to have a fasta file of my data? ...
written 7 months ago by krishnakatyal51210
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... thanks alot for this tutorial i have a vcf data file (my data)and i want to do pca how do i do that? i apologise for a naive question but i am a beginner and badly struck ...
written 7 months ago by krishnakatyal51210

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