User: Shicheng Guo

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Shicheng Guo7.6k
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Posts by Shicheng Guo

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Comment: C: WGBS alignment with BitMapperBS
... Maybe you didn't suggest the best reviewers. Sure. different people have different comments to same tools. You need to find some experts who appreciate your tools. ...
written 16 hours ago by Shicheng Guo7.6k
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gdc-client download: ERROR: Max retries exceeded
... Very interesting. It is the first time I met such problem when I use gdc-client to download TCGA dataset. gdc-client download -m gdc_manisfest.txt ERROR: Max retries exceeded. ERROR: Max retries exceeded. ERROR: Max retries exceeded. ERROR: Max retries exceeded. ERROR ...
gdc-client gdc download written 1 day ago by Shicheng Guo7.6k
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Comment: C: WGBS alignment with BitMapperBS
... Nature Protocol? Nature Method? Nucleic Acid Research? You can suggest Devon Ryan as one of the preferred reviewers. ...
written 1 day ago by Shicheng Guo7.6k
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Forum: WGBS alignment with BitMapperBS
... Now, it is time to try a faster WGBS alignment tool: [BitMapperBS][1] ./bitmapperBS --index human_genome.hg38.fa trim_galore --paired read_1.fq read_2.fq ./bitmapperBS --search human_genome.hg38.fa --seq1 read1.fq --seq2 read2.fq -t 6 --bam -o output.bam MethylDackel extract refer ...
forum bitmapperbs bismark written 5 days ago by Shicheng Guo7.6k
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Comment: C: Is it possible to generate a single maf file from multiple vcf files using vcf2m
... Why not just apply vcf2maf to individual file and then merge all the maf with sample id index? ...
written 14 days ago by Shicheng Guo7.6k
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Comment: C: generate oncoprint from input VCF file
... Any update to the problem? ...
written 18 days ago by Shicheng Guo7.6k
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Comment: C: where can I download the gold standard datasets with validated and accurate tumo
... [Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants][1] [1]: https://academic.oup.com/bioinformatics/article/34/12/2004/4827681 ...
written 19 days ago by Shicheng Guo7.6k
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Comment: C: Extracting super-population allele frequencies from 1000 genomes (phase 3) data
... As I knew, you don't need to do it by yourself. Gnomad have done it in his VCF files and you just need to extract this information. https://gnomad.broadinstitute.org/downloads ...
written 26 days ago by Shicheng Guo7.6k
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bcftools view: index -R not better than -T
... It looks index bed file don't provide better performance for `bcftools view`. method 1: `bcftools view -T` time(bcftools view -T ../chr22.SNP.bin.bed ../../chr22.1kg.phase3.v5a.vcf.gz -Oz -o chr22.SNP.vcf.gz) real 2m33.106s user 2m32.641s sys 0m0.293s method 2: `bcfto ...
-r -t bcftools written 26 days ago by Shicheng Guo7.6k
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Comment: C: How to do data cleaning for VCF genetic file
... the remaining task includes: Statistics: Alternative allele frequency > 0.5 sites: 387,454 Reference Overlap: 93.55% Match: 2,010,797 Allele switch: 0 Strand flip: 0 Strand flip and allele switch: 0 A/T, C/G genotypes: 0 Filtered sites: Filter flag set: ...
written 26 days ago by Shicheng Guo7.6k

Latest awards to Shicheng Guo

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Popular Question 4 months ago, created a question with more than 1,000 views. For Software and algorithm for identification of tissue-specific express genes
Popular Question 4 months ago, created a question with more than 1,000 views. For Software and algorithm for identification of tissue-specific express genes
Popular Question 5 months ago, created a question with more than 1,000 views. For Software and algorithm for identification of tissue-specific express genes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: error in running R

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