User: Cindy

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Cindy0
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Posts by Cindy

<prev • 25 results • page 1 of 3 • next >
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vcftools filter Allele frequency for polyploid variants
... Hi all, I have vcf files for mitochondrial DNA, which is polyploid. I want to filter out some variants based on the AF. I tried vcftools, it showed not supported. Anyone knows how to do that? Appreciate ahead ...
sequencing written 4 days ago by Cindy0
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picard MarkDuplicates error
... Hi, I have got a wired error from picard. When I run MarkDuplicates for single file, it works. But when I run multiple files, it shows error as following. Is this because too many files? or something wrong with the virtual box? I am running thin on Ubuntu on VM (host: win 10) Exception in threa ...
sequencing written 28 days ago by Cindy0 • updated 28 days ago by genomax32k
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Add head to coverage output for many files
... Hi, all, I used samtools depth to output read depth for all samples, those files have three columns but no head. I want to merge all samples together to calculate the mean read depth and sd, so I need to add sample name as a header before merge them together. When I use echo, it also output ref po ...
sequencing written 29 days ago by Cindy0 • updated 29 days ago by James Ashmore1.9k
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Python error for variant call
... Dear all, I got a error when output VCF file. "in VCFoutput i.INFO['AC'][index] += 1 IndexError: list index out of range" Here is the part where error from: for x in xrange(len(variant[3])): if variant[3] ...
assembly written 6 weeks ago by Cindy0 • updated 6 weeks ago by Istvan Albert ♦♦ 73k
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power calculation for target sequencing and survival data
... I am wondering whether there is a tool can used to calculate power for target sequencing in a case-cohort data. I have a case-cohort with target sequencing data. They are all cancer patients with several years of follow up. I will use some cancer biomarkers (continuous or category data) as outcome, ...
sequence written 6 weeks ago by Cindy0 • updated 6 weeks ago by Sej Modha1.7k
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delete IDs from a list file
... I am using gsnap for alignment. I have several hundreds of paired fastq files, So I use ls to put them in a sampleID then align one by one. sampleID=$(ls *fastq | awk 'BEGIN{FS="."}{count[$1]++}END{for(j in count) print j}') for i in $sampleID; do... However, after one week running, my co ...
alignment written 7 weeks ago by Cindy0 • updated 7 weeks ago by Pierre Lindenbaum96k
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Comment: C: MToolBox mapExome.py error
... I tried to disable "if not os.path.exists(folder): os.mkdir(folder)" in mapExome.py, line 66. Then the script can go through, but no reads assembled.My guess is the issue is in mapExome.py. But I don't know how to fix it. #!/usr/bin/python """ Written by Ernesto Picardi - e.picard ...
written 11 weeks ago by Cindy0 • updated 11 weeks ago by genomax32k
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MToolBox mapExome.py error
... I am using MToolBox to analysis mtDNA NGS data. When it runs mapExome.py for alignment, always showing error: EXECUTING READ MAPPING WITH MAPEXOME... mapExome for sample F-00-02-44707, files found: F-00-02-44707.fastq F-00-02-44707.R1.fastq F-00-02-44707.R2.fastq F-00-02-44707.fast ...
alignment sequencing written 11 weeks ago by Cindy0 • updated 11 weeks ago by genomax32k
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Comment: C: MToolBox.sh: line 173: check_files.py: command not found
... Yes. It is. GATK and SamToFastq.jar are in the same folder (ext_tools). fastq files have been successfully generated. But IndelRealigner command not found. ...
written 12 weeks ago by Cindy0
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Comment: C: MToolBox.sh: line 173: check_files.py: command not found
... After a couple of hours running, it showed another error: IndelRealigner command not found. I have already cp theGenomeAnalysisTK.jar to MToolBox/ext_tools. Any idea? Thanks ...
written 12 weeks ago by Cindy0

Latest awards to Cindy

Scholar 12 weeks ago, created an answer that has been accepted. For A: MToolBox.sh: line 173: check_files.py: command not found

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