User: noshadho

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noshadho0
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Posts by noshadho

<prev • 6 results • page 1 of 1 • next >
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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 4 weeks 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 4 weeks ago by noshadho0
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Comment: C: htslib: undefined reference Error
... Adding -lhts solved the problem, thanks :) ...
written 9 weeks 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 9 weeks 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 10 months ago by noshadho0 • updated 10 months ago by Kevin Blighe63k
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Recurrent CNV analysis
... Hello everyone, I am working on WGS data, and I am interested to do some copy number analysis. Particularly, I am looking to see what regions of genome has been applified (or deleted) recurrently in a specific cancer cohort. I know there is a tool for this called GISTIC 2.0, but it has been develop ...
gistic gene copy number variation cnv written 11 months ago by noshadho0 • updated 11 months ago by Kevin Blighe63k

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