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Recent Replies
Comment: Problem in getting geo file through GEOQUERY
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ATpoint
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> Can you send me ftp link so I can download that soft file manually?
Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
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anasjamshed
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Thanks . I have downloaded all other files but just have problem in
Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
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ATpoint
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Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
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Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
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1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
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"Are you using correct reference?"
may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
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Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
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It works. I have added this code
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I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
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Basically this is my code:
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Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
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If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY
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bk11
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It just runs fine for me with just a single line of code.
library(GEOquery)
GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE)
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Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
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I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
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I want to get lot of files through code
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Query seems to be timing out. Try getting the file directly here: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1145/matrix/GSE1145-GP…
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