User: lffu_0032
lffu_0032 • 40
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Posts by lffu_0032
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... 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 8 days ago by
lffu_0032 • 40
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... Hi,
Is there any tools can be used to call CNV in capture-based plasma sequencing data? Thanks a lot. ...
written 4 weeks ago by
lffu_0032 • 40
• updated
28 days ago by
Kevin Blighe ♦ 56k
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... I want to known if anyone ever done the downsampling CNV analysis and encountered this problem? ...
written 6 weeks ago by
lffu_0032 • 40
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... I use seqtk sample command ...
written 6 weeks ago by
lffu_0032 • 40
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... en, i am not very understand, can you give some detail explan? thank you a lot. ...
written 6 weeks ago by
lffu_0032 • 40
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... yes, random sampling different number of reads from a full fq data to see which depth is enough to call cnv. ...
written 6 weeks ago by
lffu_0032 • 40
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... 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 6 weeks ago by
lffu_0032 • 40
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... 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 6 weeks ago by
lffu_0032 • 40
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... 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 6 weeks ago by
lffu_0032 • 40
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copy number became inaccurate when downsampling different number fastq reads from a whole fastq file
... Hi, everyone:
Recent i am doing CNV analysis, i find a strange thing:
1.when using whole data (after removed dup, for tumor and its control), the copy number value is accurate;
2.but when downsample different fq reads from the whole fq for a certain sample (I just downsample the tumor's fq, and ...
written 6 weeks ago by
lffu_0032 • 40
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For what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
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