User: mikko.arvas

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Posts by mikko.arvas

<prev • 3 results • page 1 of 1 • next >
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problem using ensemblVEP with GRC37
... Hi, I would like to run ensemblVEP (without cache) with a list SNPs in a project that runs with human genome version 37. On command line this works fine: $ vep -i some.vcf --database --assembly GRCh37 --port 3337 'vep' instructs me to use '--port 3337': "If using human GRCh37 add "--port 3337" ...
ensemblvep grch37 written 2.4 years ago by mikko.arvas0
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Comment: C: How to get GenomicAlignments to read all reads?
... Thank you Mike! > bam <- readGAlignmentPairs("test.bam") > cvg <- coverage(bam) > max(cvg$`6`) [1] 1 Wrong. > bam <- readGAlignments("test.bam") > cvg <- coverage(bam) > max(cvg$`6`) [1] 50 OK! This is what I see with Baseplayer https://www.cs.helsinki.fi/u/rkataine ...
written 2.7 years ago by mikko.arvas0
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How to get GenomicAlignments to read all reads?
... Hi, when looking at a bam with a genome viewer I see reads of: -Mapping quality  over 60 -Insert size 170 kbp -Cigar 100M -Paired -Primary alingment TRUE When trying to read them to R: > sbf <- scanBamFlag(isPaired = NA, isProperPair = NA, isUnmappedQuery = NA, +             hasUnmappedMat ...
genomicalignments bam scanbamparam written 2.7 years ago by mikko.arvas0

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