User: lffu_0032

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lffu_003250
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Posts by lffu_0032

<prev • 34 results • page 1 of 4 • next >
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Answer: A: Errors in BED line using samtools bedcov
... the problem is that the naming of Chr in BED and BAM is not same. for example, if the first chr column in your BED is chr1/chr2/chr3..., and the chr column in your bam file is 1/2/3..., then you will meet this "Error in BED line" error. ...
written 27 days ago by lffu_003250
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Answer: A: Panel of tumors for CNV detection
... In order to call CNV using catpure daga, you must need the normal or panel or normal data. the tumor data is so complex for its purity and ploidy, so the tumor data is not suit for being the control. ...
written 6 months ago by lffu_003250
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capture-based plasma cnv calling
... Hi, Is there any tools can be used to call CNV in capture-based plasma sequencing data? Thanks a lot. ...
plasma capture-based cnv panel data written 7 months ago by lffu_003250 • updated 7 months ago by Kevin Blighe65k
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Comment: A: copy number became inaccurate when downsampling different number fastq reads fro
... I want to known if anyone ever done the downsampling CNV analysis and encountered this problem? ...
written 7 months ago by lffu_003250
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... I use seqtk sample command ...
written 7 months ago by lffu_003250
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... en, i am not very understand, can you give some detail explan? thank you a lot. ...
written 7 months ago by lffu_003250
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... yes, random sampling different number of reads from a full fq data to see which depth is enough to call cnv. ...
written 7 months ago by lffu_003250
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Comment: C: copy number became inaccurate when downsampling different number fastq reads fro
... I do not use any thrid-party tools. i just use very simple method: use mean depth normalization to adjust the library size effect, ant calculate the normalized value (depth/mean_depth) for tumor and normal samples, sepeartely. for normal sample, i do not downsampling reads, so the normalized value f ...
written 7 months ago by lffu_003250
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Comment: A: copy number became inaccurate when downsampling different number fastq reads fro
... i just use mean depth normalization method to adjust sequencing library size, normalized_depth = target_depth/mean(target_depth), i find for some genes, with smaller downsampling reads, the normalized_depth becames smaller, and for some genes, with smaller downsampling reads, the normalized_depth be ...
written 7 months ago by lffu_003250
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Comment: C: copy number increase or decrease WHEN downSample different number fastq reads fr
... we are doing plasma cfDNA sequencing, the sequencing depth is very high (about 10000X-30000X), we want to determine which sequencing depth is enough to call CNV accurately, so we had sequenced some cfDNA samples with ~30000X, and then downsampling to 10000X、15000X、20000X to see which depth is ok to ...
written 7 months ago by lffu_003250

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