User: mkaushal

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mkaushal70
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3 years, 8 months ago
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Posts by mkaushal

<prev • 15 results • page 1 of 2 • next >
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Comment: C: GISTIC 2.0.23 error
... See the comment below. ...
written 3 months ago by mkaushal70
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Answer: A: GISTIC 2.0.23 error
... This is the reply I obtained in the gistic google forum: Hi Madhu, As you correctly guessed, GISTIC only works with regions that are covered by segments across all samples. The "NaN processing" removes regions that have a gap in one or more samples, which in your case is all of your data. The warn ...
written 3 months ago by mkaushal70
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Missing I values for SKAT test using PLINK/SEQ
... Hello, I am running gene based association test (version plinkseq-0.10) for a case- control study of 120 case and 90 control samples (control samples from 1000 genome- population matched). I ran skat using the following command: pseq proj --phenotype phe1 --tests skat --mask loc.group=refseq mac=1- ...
skat rare variant association analysis pseq written 8 months ago by mkaushal70 • updated 8 months ago by WouterDeCoster29k
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WES samples failing ABSOLUTE
... I am trying to determine the purity and ploidy of my WES samples using ABSOLUTE. I have normal, primary and metastasized samples. Some of the samples failed ABSOLUTE. Here is an example from the error file: > [1] "Capping 13 segs at tCR = 5.0" > > [1] "Expected copy-ratio = 0.63663" > ...
absolute wes ploidy purity written 10 months ago by mkaushal70 • updated 10 months ago by markus.riester260
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Comment: C: Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
... I think you will find this useful: https://www.biostars.org/p/92536/#92649 ...
written 10 months ago by mkaushal70
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GISTIC 2.0.23 error
... Hi, I am trying to run GISTIC analysis for 30 metastasized sample data. I ran Varscan copy number and DNACopy and made my segmentation file. When I run GISTIC I get this error: GISTIC version 2.0.23 GISTIC 2.0 input error detected: All input data were removed after NaN processing I guess GISTIC ...
gistic dnacopy copy number written 13 months ago by mkaushal70
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Comment: C: 1000 Genomes exomes as controls
... I am also working on an exome sequencing study with 122 affected samples and no controls. Could you please let me know how you eventually performed the rare variant association analysis?   ...
written 2.3 years ago by mkaushal70
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Rare variant association analysis for exome study without controls
... Hello All, I am new to rare variant association analysis for exome data. The study which I am currently working on has around 120 affected individuals but no controls. I have shortlisted variants from some genes and wanted to perform burden test/SKAT for my data. Can I use 1000 genome controls for ...
skat burden test written 2.3 years ago by mkaushal70 • updated 2.3 years ago by Jason Chen10
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Comment: C: Problems running Genome MuSiC Play
... Hi, Commands I used: #genome music calculate bmr covg step genome music bmr calc-covg --bam-list tumor_bam_list.txt --output-dir results --reference-sequence hg19.fa  --roi-file hg19_coding_exons_plus10_exclude.bed --cmd-prefix qsub --gene-covg-dir results #genome music calculate bmr  step genom ...
written 3.0 years ago by mkaushal70
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Comment: C: cn.mops - Error in if (n > 512) n <- 2^ceiling(log2(n))
... I used mode="paired" in getSegmentReadCountsFromBAM and still am getting this error. This is how my seqlevels look like: > seqlevels(X)  [1] "chr1"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr2"  "chr20" "chr21" "chr22" "chr3"  "chr4"  "chr5"  "chr6"  "c ...
written 3.3 years ago by mkaushal70

Latest awards to mkaushal

Popular Question 4 weeks ago, created a question with more than 1,000 views. For GISTIC 2.0.23 error
Scholar 3 months ago, created an answer that has been accepted. For A: GISTIC 2.0.23 error
Popular Question 13 months ago, created a question with more than 1,000 views. For Problems running Genome MuSiC Play
Popular Question 21 months ago, created a question with more than 1,000 views. For Problems running Genome MuSiC Play
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Confusion with Varscan somatic filters

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