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User: Nich

gravatar for Nich
Nich • 10
Reputation:
10
Status:
New User
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Last seen:
1 day, 20 hours ago
Joined:
2 years, 1 month ago
Email:
h*******@foxmail.com

Posts by Nich

<prev • 8 results • page 1 of 1 • next >
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Distinguish tumor or normal type from WES data
... I have a set of paired tumor and normal WES next generation sequencing data. I would like to ask if there is a way I can make accurate judgments when I don't know the type of data? I would like to find a way to know whether a sample is tumor or normal without knowing their types. Can anyone help m ...
wes written 11 days ago by Nich • 10 • updated 9 days ago by Kevin Blighe ♦ 69k
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Comment: C: igv different width on reference gene exon
... I don't know why the pic can not display well ………… I share the pic on a pic website https://freeimage.host/i/21SeTu ...
written 3 months ago by Nich • 10
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igv different width on reference gene exon
... ![enter image description here][1] Hey guys I used igv to check a WES bam file. When I looked to EGFR gene, I saw that the refseq genes with blue thicker bar had a better coverage of reads. However there is little read on the blue thinner bar region. I thought all blue bar region was exon. Now ...
igv written 3 months ago by Nich • 10 • updated 3 months ago by Jorge Amigo ♦ 12k
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Comment: C: qualimap error:Exception in thread "main" java.awt.AWTError: Can't connect to X1
... Thanks for your answer! Because I want to use qualimap in my pipline, I hope that qualimap can not display the graphical interface and run the complete process directly in the background. Is there a solution for this? ...
written 16 months ago by Nich • 10
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qualimap error:Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using 'localhost:22.0' as the value of the DISPLAY variable.
... I encountered this error during the use of qualimap: > Exception in thread "main" java.awt.AWTError: Can't connect to X11 > window server using 'localhost:22.0' as the value of the DISPLAY > variable. I found the relevant solution on the official website of [qualimap][1], but I don't know ...
x11 qualimap written 16 months ago by Nich • 10 • updated 16 months ago by Pierre Lindenbaum ♦ 133k
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Comment: C: Why call variant generate homozygous site with genotype 0/0, why it be reporte
... I just use gatk HaplotypeCaller call one sample ...
written 21 months ago by Nich • 10
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Comment: C: Why call variant generate homozygous site with genotype 0/0, why it be reporte
... gatk gatk-4.1.0.0 HaplotypeCaller /software/gatk4.0/gatk-4.1.0.0/gatk --java-options '-Xmx20g' HaplotypeCaller -L region.bed -R ucsc.hg19.fasta -I ccr.bam -O ccr.vcf >ccr.std 2>&1 nothing special ...
written 21 months ago by Nich • 10
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Why call variant generate homozygous site with genotype 0/0, why it be reported even if it same with reference genome?
... Hi, guys I use gatk to call variant and get a vcf file. When I look into it, I find some homozygous site with genotype 0/0. chr2 231861039 . CCT . 793 . AN=2;DP=275;MQ=60.00 GT:AD:DP 0/0:275:275 I think this variant means it same with reference gen ...
snp written 21 months ago by Nich • 10 • updated 21 months ago by d-cameron • 2.3k

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