User: lyz10302012

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lyz10302012310
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5 months ago
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Posts by lyz10302012

<prev • 37 results • page 1 of 4 • next >
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6 follow
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GEM index fatal error
... Hi, I am trying to run GEM to create mappability file and get the following errors. I wonder if someone can give me a solution. gem-indexer -i GRCh38_full_analysis_set_plus_decoy_hla.fa -o hg38_index Creating sequence and location files...Fatal error: exception Failure("Command 'echo ...
software error written 5 months ago by lyz10302012310 • updated 28 days ago by iAmphioxus0
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local de novo assembly and split-read alignment at known sites and output bams?
... Given a set of candidate snvs and indels, is there any tools to be able to perform local de novo assembly and split-read alignment and output small bams (correct bams after assembly or split-read alignment) at these selected sites? ...
indel snv written 22 months ago by lyz10302012310 • updated 22 months ago by Devon Ryan84k
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Where is the ground truth set of SCNAs for TCGA Mutation/Variation Calling Benchmark 4?
... Hi, Can anyone tell me how can I find the ground truth set of SCNAs for TCGA Mutation/Variation Calling Benchmark 4? ...
scna ground truth set written 2.5 years ago by lyz10302012310
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Are all CNAs of HCC1153 cell line reported by COSMIC somatic mutations?
... I am using HCC1153 and HCC1954 from TCGA Mutation/Variation Calling Benchmark 4 for benchmarking SCNA calling. However, I found some SCNAs reported by COSMIC are germline CNVs (both tumor and normal sample has 0 copy (no reads) by viewing bams with IGV). Can anyone tell me how can I find the ground ...
tcga benchmark 4 written 2.5 years ago by lyz10302012310
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Can ABSOLUTE use bam file as input?
... I want to use ABSOLUTE to infer tumor purity and ploidy, but I have a question for the input. Can ABSOLUTE work for WGS bams? If not, how can I convert the bam to the input needed by ABSOLUTE? http://www.broadinstitute.org/cancer/cga/absolute_run ...
tumor written 2.9 years ago by lyz10302012310 • updated 2.9 years ago by Lemire/OICR370
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Answer: A: How to draw venn diagram for two CNV lists?
... Here my question is how to determine the intersect, is it 10 or 20? ...
written 3.8 years ago by lyz10302012310
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How to draw venn diagram for two CNV lists?
... I want to draw the venn diagram for two CNV lists. I use a 1-bp reciprocal overlap criterion to declare two CNVs are same. My question is if one element in list 1 overlaps with multi elements in list 2, how can I interpret intersect? i.e. Size of list1: 100 Size of list2: 200 10 CNVs in list1 o ...
venn tool written 3.8 years ago by lyz10302012310 • updated 4 weeks ago by lieven.sterck2.4k
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(Closed) Jointly Detect Somatic Copy Number Variations
... Hi, Is there any good tools to jointly detect somatic copy number variations (like some tools for SNVs) from tumor-normal paired sequencing data? If not, how can I detect somatic copy number variations using existing common CNV detecting tools? Thanks ...
written 4.6 years ago by lyz10302012310 • updated 4.6 years ago by Chris Miller20k
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What Is The Ratio Of Heterozygous Vs. Homozygous In An Individual?
... Can anyone tell me what is the ratio of heterozygous SNPs/INDELs/SVs vs. homozygous SNPs/INDELs/SVs in an individual? ...
variant written 4.8 years ago by lyz10302012310 • updated 2.3 years ago by Shab86220
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Where Can I Download Venter Genome'S Structural Variants (Hg19 Or Build 37)?
... Hi, Can anyone tell me where can I download Venter Genome's structural variants (hg19 or build 37)? Thanks, Eric ...
written 4.8 years ago by lyz10302012310

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Popular Question 22 months ago, created a question with more than 1,000 views. For Can ABSOLUTE use bam file as input?
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Great Question 2.9 years ago, created a question with more than 5,000 views. For How To Sort Bed Format File
Good Question 2.9 years ago, asked a question that was upvoted at least 5 times. For How To Sort Bed Format File
Epic Question 2.9 years ago, created a question with more than 10,000 views. For How To Sort Bed Format File
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Open Source Java De Novo Assembly Software
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Popular Question 3.8 years ago, created a question with more than 1,000 views. For Open Source Java De Novo Assembly Software
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