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User: Sara

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Sara • 150
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150
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4 years, 4 months ago
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Posts by Sara

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Comment: A: UMI and the reason of high duplicate rate
... yes at the UMI level we have high duplication rate. ...
written 6 weeks ago by Sara • 150
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UMI and the reason of high duplicate rate
... in our RNA-seq data (UMI is used) we have generated we have very high duplicate rate (after removing UMI and duplicate we would have only 10 % of the reads). can you let me know what metrices I can collect to investigate the problem? ...
rna-seq written 6 weeks ago by Sara • 150 • updated 6 weeks ago by swbarnes2 ♦ 9.1k
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compare expression for 1 gene between more than 2 samples
... what is the best way to compare expression for 1 gene between > 2 samples? FPKM/RPKM/TPM/CPM or log2 FC ...
rna-seq written 7 weeks ago by Sara • 150 • updated 7 weeks ago by noahhelton98 • 0
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correct order for pathway analysis
... I am doing pathway analysis but there a lot of tutorials so, I am looking for the correct way of doing that. 1- I got DE genes (up and down regulated) 2- filter them based on log2 of FC. only the genes with Log2FC > 1 or Log2FC < -1 are used for pathway analysis 3- I used up and ...
gene written 11 weeks ago by Sara • 150
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a lot of missing variants when using DRAGEN for variant calling
... I have to use `DRAGEN` for small variant calling and generating `VCF` files. at this step I am doing `benchmarking` to see the results of that. my colleague have done the same analysis using GATK3. then I compared the sites in my vcf file (made using `DRAGEN`) and the vcf file which was made using ` ...
next-gen written 12 weeks ago by Sara • 150
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comparing 2 VCF files
... I am trying to compare two VCF file (results of small variant calling from WES data) to get overlapping and non-overlapping regions separately. what is the best tool for this comparison? ...
snp written 12 weeks ago by Sara • 150
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building container in singularity
... I have some script in a folder and trying to make a `singularity` image (container) for them using the following command: sudo singularity build production.sif /home/Desktop/test/ and here in the output on shell: [sudo] password for john: Building image from sandbox: /home/Desktop/t ...
software error written 3 months ago by Sara • 150
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Comment: C: unmapped reads in FFPE samples
... bowtie and once STAR. ...
written 3 months ago by Sara • 150
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VCF evaluation using RTG.jar vcfeval
... Hi there, I am trying to do benchmarking for my pipeline (to analyze `WES` and `WGS` `germline` and generate VCF file for `SNV and INDELs`). to do so, I got the WES data for this sample from hare: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSe ...
snp written 4 months ago by Sara • 150 • updated 4 months ago by Len Trigg • 1.5k
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missing file in rtg-tools
... I am trying to use rtg tool (specifically `rtg.jar`). I got the tool from here: https://www.realtimegenomics.com/products/rtg-tools and unzipped that. in this directory : `tools/rtg-tools/installer/` I can see the following files: README.txt ReleaseNotes.txt resources rtg rtg.bat rtg. ...
snp written 4 months ago by Sara • 150

Latest awards to Sara

Popular Question 11 weeks ago, created a question with more than 1,000 views. For DE analysis using single cell RNA-seq data
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