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Recent Replies
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
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50
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
by
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)
…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
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Dave Carlson
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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 …
Comment: Problem in getting geo file through GEOQUERY
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I want to get lot of files through code
Comment: Problem in getting geo file through GEOQUERY
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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…
Comment: Add stats to the plot
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Thanks for the help. Unfortunately, did not work :(
error in asserttat_group_columns_exists(data) :
data should contain group1 and grou…
Comment: downloading chemical database from ChEMBL
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How about following
https://www.ebi.ac.uk/chembl/web_components/explore/activities/ --> Select a compound --> Related Targets button --> D…
Comment: Genotyping sites with N in reference genome
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As a follow-up, is it possible to get a variant call with UnifiedGenotyper if rather than N, I have one of the ambiguity codes (e.g. R, Y, …
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The GATK (and afaik every caller that I know) treats every contig of the reference as having the same ploidy (so all haploid, all diploid, …
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Use the sequence Illumina recommends for the specific kit.
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> Thanks. What determines what constitutes a good distance?
I think tools like BWA use the median distance for each chunk of processed d…
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bioinfo
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Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
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mrk
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Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are pai…
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Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
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Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
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