User: Nich
Nich • 10
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Posts by Nich
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... 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 ...
written 11 days ago by
Nich • 10
• updated
9 days ago by
Kevin Blighe ♦ 69k
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... 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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... ![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 ...
written 3 months ago by
Nich • 10
• updated
3 months ago by
Jorge Amigo ♦ 12k
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... 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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... 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 ...
written 16 months ago by
Nich • 10
• updated
16 months ago by
Pierre Lindenbaum ♦ 133k
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... I just use gatk HaplotypeCaller call one sample ...
written 21 months ago by
Nich • 10
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... 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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... 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 ...
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