User: noshadho

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noshadho0
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Posts by noshadho

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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 14 days ago by noshadho0
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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 24 days ago by noshadho0 • updated 23 days ago by markus.riester500
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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 weeks ago by noshadho0
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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 weeks ago by noshadho0
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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 9 weeks ago by noshadho0
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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 3 months ago by noshadho0
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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 3 months ago by noshadho0
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Comment: C: htslib: undefined reference Error
... Adding -lhts solved the problem, thanks :) ...
written 4 months ago by noshadho0
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htslib: undefined reference Error
... Hi Everyone, I've been stuck with this problem for over a day now and I searched everywhere, I couldn't find any solution for this problem. I am trying to use htslib and I have a very simple code: #include #include #include "/data/miniconda3/include/htslib/vcf.h" #include "/data ...
vcf C c++ samtools htslib written 4 months ago by noshadho0
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GISTIC 2.0 markers
... Hi all, I am using GISTIC2.0 for a segmented file I have (Segmented using CBS). I can't understand what is marker file. What does a marker represent here? how dp we choose markers? Thanks ...
gistic marker cnv segmentation bioinformatics written 13 months ago by noshadho0 • updated 13 months ago by Kevin Blighe66k

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