User: lzy

gravatar for lzy
lzy20
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3 months, 2 weeks ago
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2 years, 4 months ago
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l**@bioinfo.org

Posts by lzy

<prev • 9 results • page 1 of 1 • next >
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Comment: C: mutational signatures in different tumor samples
... Does anyone know how to identify the mutation signatures I want? ...
written 5 months ago by lzy20
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mutational signatures in different tumor samples
... Dear all. I am currently researching the mutational signatures (or patterns?) in a large cohort of targeted sequencing of tumor samples. I found that the definition of "mutational signatures" in COSMIC is like this : "The profile of each signature is displayed using the six substitution subtypes: C& ...
mutational signature somatic mutation written 5 months ago by lzy20 • updated 5 months ago by RamRS22k
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Comment: C: Where to get homopolymer annotation for human genome ?
... Thank you very much, I will try this method. ...
written 11 months ago by lzy20
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Comment: C: Where to get homopolymer annotation for human genome ?
... Thank you very much, I have tried your R script for homopolymer finding, and got result as follow: > PolyAll6_hg19 GRanges object with 7760901 ranges and 0 metadata columns: seqnames ranges strand [1] ...
written 11 months ago by lzy20
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Where to get homopolymer annotation for human genome ?
... I got lots of SNV and Indel somatic mutations from whole genome sequencing data from tumor. And I want to annotate these somatic mutations with whether located in the homopolymer region of human genome. I have already search the ucsc repeatmasker track, and it does not contain homopolymer annotati ...
annotation homopolymer snp written 11 months ago by lzy20 • updated 21 days ago by bioinfo8940
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Comment: C: Do I need to test the repeatability and reproducibility of a fixed bioinformati
... Hi, Nandini. Thanks for your answer. The specificity and sensitivity can be evaluated by running the pipeline on the benchmark data. I want to know do I need to run the pipeline on the same benchmark data 2-3 times to evaluate the repeatability and reproducibility of the pipeline. In my opinion, ru ...
written 12 months ago by lzy20
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Comment: C: Do I need to test the repeatability and reproducibility of a fixed bioinformati
... Thanks, jnf3769. I have revised my question. I just want to know "How to evaluate the precision (repeatability and reproducibility) of a bioinformatics analysis pipeline? Or, do I need to evaluate the precision (repeatability and reproducibility) of a bioinformatics analysis pipeline?" ...
written 12 months ago by lzy20
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Do I need to test the repeatability and reproducibility of a fixed bioinformatics pipeline for SNV calling
... Next-generation sequencing based genetic testing requires proof-of-concept validation with established performance metrics before introducing into the clinical laboratory. The performance metrics evaluated to establish the analytical validity of test results include accuracy, precision, analytical s ...
next-gen snp sequencing written 12 months ago by lzy20 • updated 12 months ago by Nandini810
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Answer: A: Anyone used BAMSurgeon to spike in 1KB insertions/deletions?
... Hi Sichan, Could you tell me how get the correct BAM Alignment input file ? As I use the follow command lines: 1),bwa mem -t 2 -M hg19.fa NA12878_R1.fastq NA12878_R2.fastq > NA12878.sam 2),samtools view -bS NA12878.sam > NA12878.bam 3),java -jar SortSam.jar INPUT= NA12878.bam OUTPUT= NA1287 ...
written 2.3 years ago by lzy20

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