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User: Raheleh

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Raheleh • 50
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Posts by Raheleh

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Calling CNV using bcftools
... @Pierre Lindenbaum Dear Pierre many thanks for your reply. How can I get these two annotations for my data. Should I use another variant caller instead of VarScan2? If so, what do you recommend? ...
written 7 weeks ago by Raheleh • 50
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Calling CNV using bcftools
... Hi, I used VarScan2 to call variants from whole exome sequencing data. The vcf file output looks like this: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR chr1 972251 . A AC . PASS DP=173;SOMATIC;SS=2;SSC=75;GPV=1;SPV=2.5611e-08 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:65:63:0:0%:36,27,0,0 ...
vcf bcftools cnv written 7 weeks ago by Raheleh • 50 • updated 7 weeks ago by Pierre Lindenbaum ♦ 118k
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Comment: C: Problem in converting vcf to maf using vcf2maf tools
... @Kevin Blighe I ran this command bcftools cnv -c normal_rmdup.bam -s tumor_rmdup.bam -o outdir/ -p 0 Somatic.hc.fpfilterPassed.vcf to produce a plot of my CNV file but I got this error: `The sample "tumor_rmdup.bam" not found` The sample exist in the same directory as others. What's the pr ...
written 7 weeks ago by Raheleh • 50
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Comment: A: Problem in converting vcf to maf using vcf2maf tools
... Is there any other ways to convert vcf to maf? ...
written 7 weeks ago by Raheleh • 50
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Comment: C: Problem in converting vcf to maf using vcf2maf tools
... Oh, yeah. I did exactly as it is said [here][1] , so I think the path must be this `export VEP_DATA=$HOME/.vep`, right? when I open terminal in the folder that I installed VEP, it shows this path: **~/vep** [1]: https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697 ...
written 7 weeks ago by Raheleh • 50
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Comment: C: Problem in converting vcf to maf using vcf2maf tools
... @h.mon Thank you. I defined it with `export VEP_DATA=/path/to/vep/data` but now the error changed to this: bash: /path/to/vep/data/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz: No such file or directory can you please help me? ...
written 7 weeks ago by Raheleh • 50
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Problem in converting vcf to maf using vcf2maf tools
... Hi, I want to convert my vcf file (VarScan output) to maf file to generate some publication-quality images using maftools (R package). Based on the instruction of vcf2maf tools [here][1], I installed VEP. But when I ran this command: perl vcf2maf.pl --ref-fasta /home/raheleh/.vep/homo_sapiens ...
varscan grch38 vcf2maf written 7 weeks ago by Raheleh • 50
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How to annotate Copy Number Variations (Output of VarScan2)
... Hi, I ran this command: samtools mpileup -q 1 -f hg38.fa normal.sorted.bam tumor.sorted.bam | java -jar VarScan.v2.4.3.jar copynumber varScan --mpileup 1 and this is a part of the output: > chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content & ...
varscan cnv annotation written 8 weeks ago by Raheleh • 50 • updated 8 weeks ago by Pierre Lindenbaum ♦ 118k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Hi, many thanks for the great tutorial. This command doesn't work for me: `z = [(value gene X in tumor Y)-(mean gene X in normal)]/(standard deviation X in normal)` It returns this error: > Error: unexpected '[' in "z = [" Can you help me solve it? Thanks! ...
written 9 weeks ago by Raheleh • 50
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Problem in installing mclust package R
... Hello, I tried to install mclust package R in RStudio using different ways install.packages("mclust") devtools::install_github("cran/mclust") biocLite('mclust') but I get this error: * installing *source* package ‘mclust’ ... ** package ‘mclust’ successfully unpacked and MD ...
R lgfortran mclust written 3 months ago by Raheleh • 50 • updated 3 months ago by Jean-Karim Heriche ♦ 18k

Latest awards to Raheleh

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
Student 5 months ago, asked a question with at least 3 up-votes. For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question 15 months ago, created a question with more than 1,000 views. For Why some probes have "NA" for gene symbol and Entrez ID?
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