User: nitinra

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nitinra10
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Posts by nitinra

<prev • 17 results • page 1 of 2 • next >
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Different estimates of nucleotide diversity (pi) from two pipelines: pixy vs vcftools
... Hello all, I am trying to calculate nucleotide diversity on 192 samples and have used vcftools and pixy to calculate it. However, the results from both pipelines are dissimilar. Is there a way to evaluate which one is the accurate estimate of nucleotide diversity? Here is the pipeline I used: ...
pixy vcftools nucleotide diversity written 28 days ago by nitinra10
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Comment: C: Back-filling missing genotypes in merged VCF
... Hello, I tried running this command and got this: [SEVERE][Launcher]There was an error in the command line arguments. Please check your parameters : Expected one or zero argument but got 2 : [bams.txt, merged_filtered_sort.recode.vcf] What can I do to resolve this? ...
written 5 weeks ago by nitinra10
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Comment: C: How to generate a tab limited genome co-odinate file from a reference - bedtools
... thank you so much! I don't think I was using the right keywords. I completely missed this! ...
written 5 weeks ago by nitinra10
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Answer: A: Nucleotide diversity between population
... Hi, it depends on what your question is. You can do a nucelotide diversity on whole genomes within populations and then compare it between populations. You can use R to then plot how it differs along each chromosome. Here is a [post][1] explaining it (the explanation is in Mandarin), but the codes a ...
written 5 weeks ago by nitinra10
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How to generate a tab limited genome co-odinate file from a reference - bedtools
... Hello all, I am trying to generate a genome file similar to [this][1] from a fasta reference genome. What tool can I use to generate this? Thank you. [1]: https://github.com/arq5x/bedtools2/blob/master/genomes/mouse.mm9.genome ...
genome bedtools snp written 5 weeks ago by nitinra10
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How to setup a mac for genomic analysis
... Hello all, I have been doing all my genomic analysis on a remote cluster so far and it works perfectly for me. However, there are times when I wish I could run it on my own computer (since I have to request permissions every time to install modules etc). I have a macbook pro and I am looking for a ...
next-gen software installation written 5 weeks ago by nitinra10 • updated 5 weeks ago by GenoMax95k
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Comment: C: Merge CNVnator and Lumpy to find out copy number variants
... Do you know what format the genome file size should be for bedpe_sort.py? I tried using the reference file in fasta format and it returned a blank file. ...
written 5 weeks ago by nitinra10
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Determining breakpoint size in cnvnator-lumpy pipeline
... Hello all, I am trying to pipe the results from CNVnator to lumpy using the cnvnator_to_bedpes.py ([lumpy git code][1]) I am not sure how to determine the breakpoint size for the input. How do I determine the breakpoint size? Is it the same as the bin size used during cnvnator CNV calling? Thank ...
sv cnvnator lumpy cnv written 6 weeks ago by nitinra10
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Pipeline for merging vcf files from lumpy and cnvnator and sv filtering
... Hello all, I have obtained vcf output files from running lumpy and cnvnator. I am looking for a way/pipeline to merge vcf files from both these pipelines into one. Can I use the same tools that are used for SNPs (such as bedtools, bcftools) to merge these vcf files or is there a pipeline specific t ...
sv wgs cnv written 6 weeks ago by nitinra10
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How to distinguish selection vs population demography from Tajima's D test
... Hi all, I have calculated genomewide Tajima's D using VCFtools --Tajima option and got a positive Tajima value (diploid organism, butterfly species). This could either mean balancing selection or population contraction. Is there a way to distinguish between the two? I have also done pairwise Fst an ...
tajima vcf snp population genetics written 3 months ago by nitinra10 • updated 3 months ago by h.mon32k

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