User: Shicheng Guo
Shicheng Guo • 7.6k
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Posts by Shicheng Guo
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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 Guo • 7.6k
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... 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 ...
written 1 day ago by
Shicheng Guo • 7.6k
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133
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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 Guo • 7.6k
14
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6 follow
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... 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 ...
written 5 days ago by
Shicheng Guo • 7.6k
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121
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... Why not just apply vcf2maf to individual file and then merge all the maf with sample id index? ...
written 14 days ago by
Shicheng Guo • 7.6k
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884
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... Any update to the problem? ...
written 18 days ago by
Shicheng Guo • 7.6k
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105
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... [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 Guo • 7.6k
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108
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... 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 Guo • 7.6k
1
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0
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127
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... 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 ...
written 26 days ago by
Shicheng Guo • 7.6k
0
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1
answer
402
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1
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... 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 Guo • 7.6k
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