User: hsbinf

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hsbinf20
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Posts by hsbinf

<prev • 13 results • page 1 of 2 • next >
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Download BAM files from TCGA/GDC Legacy Archive using a script
... Hi guys, I need to download a lot of BAM files(~200 cases) from GDC Legacy Archive that were created using Hg19. I've been doing this manually for a few cases to get the feel of the database but I'm trying to figure out if there's a script to do that? I did see the Bioconductor package Genomic Data ...
tcga gdc-legacy written 9 weeks ago by hsbinf20
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Single Cell Sequencing Quality
... I have some single cell sequencing data and I did some quick statistics on them to give feedback about the sequencing kits used (RepliG and PicoPlex). For some samples, I'm getting some discrepancies in the numbers and I was wondering if that's expected or is it an issue. Here's some data for one o ...
bedtools samtools single cell written 9 months ago by hsbinf20 • updated 9 months ago by RamRS22k
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Download example data of cancer gene-panel
... Hi guys, I want to download some targeted gene-panel sequencing data samples for cancer. Any idea where I can find these samples to download online? Fastq or bam format. Thanks! ...
fastq gene-panel bam written 13 months ago by hsbinf20 • updated 13 months ago by genomax69k
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Comment: C: Varscan somatic caller - Genotype calls
... Hi this is first line of the result after using Varscan v2.4.3 and doing processSomatic. The normal genotype is still 1/1 even though VAF is 0%. I'm just having trouble understanding why its 1/1 as 1/1 would indicate homozygous alternate but we see 0 alternate reads in the normal. Also this line i ...
written 13 months ago by hsbinf20
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Comment: C: Varscan somatic caller - Genotype calls
... Thanks! Will try that. ...
written 13 months ago by hsbinf20
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Comment: C: Varscan somatic caller - Genotype calls
... Varscan v2.3.9 Command: java -jar Varscan.jar somatic normal_pileup tumor_pileup basename --output-vcf 1 Reference file: hg19 ...
written 13 months ago by hsbinf20
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Varscan somatic caller - Genotype calls
... Hi, I used Varscan somatic to get somatic variant calls. In some SNPs, the genotype for normal sample is 1/1 and the alt read count in the normal is 0. I am wondering if this is an acceptable call? Is there a reason I'm missing why Varscan assigned 1/1 to normal despite having 0 alternate reads? ...
varscan somatic written 13 months ago by hsbinf20
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readSnpMatrix in FACETS gives error
... Hi! I'm trying to run FACETS (allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing). I created a SNP matrix using the perl script snp-pileup.pl. But when I run it in R it gives an error. rcmat <- readSnpMatrix("sample1_facets_input", skip=0L, ...
facets purity cnv ploidy written 14 months ago by hsbinf20
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Comment: C: bam-readcount installation error
... Thanks a lot ! It works now ...
written 22 months ago by hsbinf20
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Comment: C: bam-readcount installation error
... I had tried that too. Says it cannot find CMakeLists.txt That is why I ran cmake on the ./bam-readcount. Do I need to copy anything in ./repo? ...
written 22 months ago by hsbinf20

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Popular Question 8 weeks ago, created a question with more than 1,000 views. For bam-readcount installation error

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