User: rshoobs

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rshoobs10
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Posts by rshoobs

<prev • 12 results • page 1 of 2 • next >
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How can you update position field in a VCF?
... I am attempting to LiftOver a set of vcf files from hg19 to hg38. I attempted to use the `picard LiftOverVCF` tool developed by the broad institute, however I have found that the amount of required RAM is large and is not feasible on my machine. Instead I have extracted my set of SNPs from my vcf fi ...
gene written 5 days ago by rshoobs10
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Comment: C: Current standards for batch correction and gene expression correction?
... RNASeq and the batches are not known ...
written 3 months ago by rshoobs10
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Current standards for batch correction and gene expression correction?
... I am interested in running batch effect correction on my gene expression data and am looking into what the current standards are. Previously I used [PEER][1] to correct for batch effects but it is almost a decade old and does not seem to be supported on R 3.5. What are people currently using for bat ...
rna-seq written 3 months ago by rshoobs10 • updated 3 months ago by geek_y10k
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Does bcftools support any kind of large dictionary based editing of variants?
... I have a text file of snp positions that change between builds and would like to update my vcf file accordingly. I could throw the whole thing into R, but I'd like to know if bcftools has anything more convenient. Essentially I am looking for something that interfaces with the output of liftOver in ...
bcftools snp written 7 months ago by rshoobs10 • updated 7 months ago by Pierre Lindenbaum126k
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will recombination rates differ between builds of the human genome?
... I am running MOSAIC which requires something akin to recombination rate as part of their input, however my data is in a different build than their example data. Will the recombination rates change between builds of the human genome? Or can i use their provided data for my purposes? If not how can i ...
genome recombination written 8 months ago by rshoobs10 • updated 7 months ago by h.mon29k
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calculating cumulative recombination rate for MOSAIC?
... I am running MOSAIC and don't understand how their "cumulative recombination rate" is calculated. I have the 1000G genetic map that their data appears to be based off of, but don't know how to convert the combined rate to the cumulative rate. As an example the first few lines of the genetic map look ...
mosaic local ancestry recombination written 8 months ago by rshoobs10
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alternative chromosomes in liftover, what does this mean?
... I've been performing liftover from hg19 to hg38 based on genetic position using the LiftOver utility. I have several snps the chromosomes of which have been labelled as such `chr7_KI270803v1_alt`. In particular chromosomes 7 and 8 demonstrate an inordinate amount of this tagging. On further inspecti ...
genome snp written 12 months ago by rshoobs10 • updated 11 months ago by Biostar ♦♦ 20
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Comment: C: Liftover errors with CrossMap and Picard
... I've been trying further and find that it works with a bed file that I've created from my vcf. Only issue is that It doesn't preserve any mapping so i can't coordinate any genotypes! ...
written 14 months ago by rshoobs10
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Liftover errors with CrossMap and Picard
... Hi all, I am attempting to use CrossMap to convert my dosage files output from the sanger imputation service from hg19/37 to hg38. Here is the command I am using python3 ~/software/CrossMap-0.3.1/bin/CrossMap.py vcf ~/Data/liftover/hg19ToHg38.over.chain.gz 22_withMAF.vcf.gz ~/Data/GenCode/GRC ...
software error rna-seq snp written 14 months ago by rshoobs10
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Comment: C: Calculate minor allele frequency from VCF
... yes this is perfect! has a MAF option I can use ...
written 16 months ago by rshoobs10

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Popular Question 7 months ago, created a question with more than 1,000 views. For Calculate minor allele frequency from VCF

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