User: Shicheng Guo

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Shicheng Guo4.2k
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Posts by Shicheng Guo

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How to infer the target TF gene of ZNF132 without any ChIP-seq knowledge?
... Hi All, Any way I can choose to infer the target genes which are regulated by transcript factor gene: ZNF132 without any ChIP-seq result. By the way, ENCODE didn't include this gene in his ChIP-seq design. Thanks. ...
znf132 chip-seq written 5 days ago by Shicheng Guo4.2k
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Equivalent Online Tools for co-expression network construct similar with String 9.0?
... Hi All, Any Equivalent Online Tools for co-expression network construct similar with String 9.0? What I want is the co-expression network (pdf) when I input gene symbol or a gene list. like this Figure: ![enter image description here][1] Thanks. [1]: https://lh3.googleusercontent.com/-3e9m ...
string 9.0 co-expression network written 6 days ago by Shicheng Guo4.2k
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Comment: C: Extract Cg Dinucleotides Coordinates From (Human) Genome
... Script have no problem. However, input are chr1.fa chr2.fa .... and output will be chr1.CpG.positions.txt .... ...
written 17 days ago by Shicheng Guo4.2k
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Answer: A: Extract Cg Dinucleotides Coordinates From (Human) Genome
... Anyone want to validate my perl script. save this script as: cgpositionFinder.pl #!/usr/bin/perl # search the postions for the CpGs in human genome # input are chr1.fa, chr2.fa and so on # output will be chr1.CpG.positions.txt and so on. # Finally, merge all the CpG.positions.tx ...
written 19 days ago by Shicheng Guo4.2k
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The fastest BS-seq data alignment tools and setting
... Hi All, Suppose I only want to make the fast methylation-seq data alignment. Which tools or which kind of setting can give me fastest alignment to get the bam file? for example, my fastq file is 400G, I just hope to finish the alignment within one day. I can only use the maxmimu multiple-core=32 ...
bs-seq written 19 days ago by Shicheng Guo4.2k
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Answer: A: Where to download refseq gene data
... Download Human and Mouse refGene from UCSC with bash wget wget -c -O mm9.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz wget -c -O mm10.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz wget -c -O hg19.refGene. ...
written 5 weeks ago by Shicheng Guo4.2k
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Comment: C: Where to download refseq gene data
... Any SQL or Perl script to do it? ...
written 5 weeks ago by Shicheng Guo4.2k
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Comment: C: Method to Check Fastq Completeness after Fastq-dump
... By the way: how to deal with Resume Broken Download Problem for fastq-dump ? ...
written 5 weeks ago by Shicheng Guo4.2k
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Answer: A: How can I find SRA MD5 checksums for FASQ files?
... Try this one. When you didn't remove SRA files, you can use the following: for i in `ls *.gz`; do SRR=${i%%_*}; echo $SRR >> list.txt; done for j in `sort -u list.txt` do vdb-validate $j done if you have already removed SRA and only ...
written 5 weeks ago by Shicheng Guo4.2k
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Comment: C: Method to Check Fastq Completeness after Fastq-dump
... Thanks. The method you mention works in some way. However, for the majority situation, it doesn't work. for example: fastq-dump --split-files --gzip SRR949203 if you just download the SRA files, I think it is okay to use vdb-validate SRR949203 ...
written 5 weeks ago by Shicheng Guo4.2k

Latest awards to Shicheng Guo

Gold Standard 13 days ago, created a post with more than 25 bookmarks. For Good Habit for Bioinformatics Analyst or Scientist
Popular Question 19 days ago, created a question with more than 1,000 views. For fastq-dump split-spot and skip-technical
Popular Question 21 days ago, created a question with more than 1,000 views. For fastq-dump split-spot and skip-technical
Popular Question 9 weeks ago, created a question with more than 1,000 views. For fastq-dump split-spot and skip-technical
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: error in running R
Student 3 months ago, asked a question with at least 3 up-votes. For Definition and formula of methylation heterogeneity
Popular Question 3 months ago, created a question with more than 1,000 views. For fastq-dump split-spot and skip-technical
Popular Question 3 months ago, created a question with more than 1,000 views. For Gallery: Computational tools for DNA methylation
Popular Question 3 months ago, created a question with more than 1,000 views. For Fold change > 2 and P-value<0.05 in micro-array differential analysis
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Popular Question 3 months ago, created a question with more than 1,000 views. For R: heatmap for triangular matrix
Appreciated 3 months ago, created a post with more than 5 votes. For A: What is a typical workflow to correlate methylation and expression data?
Popular Question 4 months ago, created a question with more than 1,000 views. For Protocol To Downlad TCGA Data From GDC
Popular Question 4 months ago, created a question with more than 1,000 views. For R: heatmap for triangular matrix
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Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: What is a typical workflow to correlate methylation and expression data?
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