User: noshadho

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noshadho10
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Posts by noshadho

<prev • 14 results • page 1 of 2 • next >
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Comment: C: TCGA capture kits VCRome
... Thanks for your reply,I'm not sure, the most I could find about this kit was in [this][1] link, but nothing more. I'm gonna email them and write the results here [1]: https://www.irdirc.org/wp-content/uploads/2017/12/T1S2-2_YangYP.pdf ...
written 5 weeks ago by noshadho10
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TCGA capture kits VCRome
... Hi all, I am running an analysis on TCGA data and the NGS data I am using has 4 different capture kits. 2 of them are: **SeqCap EZ HGSC VCRome** and **VCRomeV2.1-PKv1**. While I can find the bed files for **SeqCap EZ HGSC VCRome**, I can't find anything on **VCRomeV2.1-PKv1**. Does anyone know ...
ngs tcga coverage capturekit written 5 weeks ago by noshadho10
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Reference Consortium (HRC) in GRch38/hg38
... Hi, I am trying to phase a tumor variants using Eagle2/Shapeit4. My sample coordinates are in Grch38/hg38, but the Haplotype Reference Consortium (HRC) coordinates are in GRch37/hg19. I was wondering does anyone know if there is a hg38 version of HRC or what are the steps to liftover it's VCF fil ...
genome haplotype reference written 4 months ago by noshadho10
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Comment: C: Combining normal+tumor fastq files to make a diluted tumor sample
... Hi Kevin, thanks for your reply, I finally managed to do it myself. What I did was to write a shell script which uses "fastq-sample" tool to uniformly sample for example 90mil reads from normal and then 10mil reads from the tumor. Then write both into one fastq (if pair end, fastq-sample will handl ...
written 4 months ago by noshadho10
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TCGA capture kits
... Hi All, I am looking to do some CNV analysis on TCGA-KIRP cohort, but I can't find the whole exome capture kit they have used for each sample. Is this information provided somewhere? where can I find it? Thanks ...
copynumbr tcga capture-kit written 4 months ago by noshadho10 • updated 4 months ago by markus.riester510
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Comment: C: GISTIC 2.0 markers
... Hi Kevin, do you use bins for your data? If I am using bins (like dividing genome into 10k, 20k, etc bins), I would pass on the number of bins each segment contains (because that is how many measurements we have for that segment). If not bins(like in a targeted panel or wxs sample), I would just pas ...
written 5 months ago by noshadho10
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From 10x single cell data to a bulk analysis
... Hi All, I have a 10x single cell dna sequence from a tumor which contains ~900 cells. Goal here is to look up the cells copy number. After some analysis on the data, We realized that cells can be cluster in two clusters based on their CNV. Now we want to do some pseudo-bulk analysis on each cluste ...
singlecell 10x dna-seq copy number cellranger written 5 months ago by noshadho10
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Cellranger cnv analysis bin size
... Hi Everyone, I have recently started to use cellranger pipeline to analyse my sequenced data. I have started with cellranger-dna mkfastq first to generate fastq files, and then used cellranger-dna cnv to generate BAM files and copy number analysis results. The problem is that "cellranger-dna cnv ...
singlecell cellranger_dna cellranger cnv written 6 months ago by noshadho10
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Answer: A: Merge several bigWig files (with different intervals) into single GRanges object
... You can make a Granges object with the tile width that you want, then by using `GenomicRanges::findOverlaps()` find the score value for each one. First you need to define your sequence info for genomic ranges object: seqi = Seqinfo("chr1",1000) # Seqinfo object with 1 sequence from an unsp ...
written 7 months ago by noshadho10
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Combining normal+tumor fastq files to make a diluted tumor sample
... Hi everyone, I have a tumor sample and it's matched normal fastq files. I consider my tumor sample contents to be ~99% pure. I am trying to dilute this tumor sample to ~10% tumor content. The idea is to make a fastq file with 90% of matched normal reads and 10% of tumor sample reads. I'd like to ...
dilution fastq tumor matchednormal cancer written 7 months ago by noshadho10

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Popular Question 3 months ago, created a question with more than 1,000 views. For GISTIC 2.0 markers

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