User: Shicheng Guo

gravatar for Shicheng Guo
Shicheng Guo4.2k
Reputation:
4,200
Status:
Trusted
Location:
Last seen:
8 hours ago
Joined:
1 year, 8 months ago
Email:
s***********@hotmail.com

Posts by Shicheng Guo

<prev • 324 results • page 1 of 33 • next >
0
votes
1
answer
934
views
1
answers
Comment: C: How to get somatic variant from TCGA vcf files
... This link is broken: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/ Maybe you can update it. ...
written 6 days ago by Shicheng Guo4.2k
1
vote
0
answers
105
views
0
answers
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 weeks ago by Shicheng Guo4.2k
0
votes
0
answers
65
views
0
answers
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 5 weeks ago by Shicheng Guo4.2k
0
votes
2
answers
1.7k
views
2
answers
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 7 weeks ago by Shicheng Guo4.2k
0
votes
2
answers
1.7k
views
2
answers
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 7 weeks ago by Shicheng Guo4.2k
0
votes
1
answer
160
views
1
answer
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 7 weeks ago by Shicheng Guo4.2k
1
vote
2
answers
2.1k
views
2
answers
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 10 weeks ago by Shicheng Guo4.2k
0
votes
2
answers
2.1k
views
2
answers
Comment: C: Where to download refseq gene data
... Any SQL or Perl script to do it? ...
written 10 weeks ago by Shicheng Guo4.2k
0
votes
0
answers
169
views
0
answers
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 10 weeks ago by Shicheng Guo4.2k
0
votes
4
answers
1.8k
views
4
answers
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 10 weeks ago by Shicheng Guo4.2k

Latest awards to Shicheng Guo

Popular Question 4 weeks ago, created a question with more than 1,000 views. For How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
Gold Standard 6 weeks ago, created a post with more than 25 bookmarks. For Good Habit for Bioinformatics Analyst or Scientist
Popular Question 7 weeks ago, created a question with more than 1,000 views. For fastq-dump split-spot and skip-technical
Popular Question 8 weeks 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 fastq-dump split-spot and skip-technical
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: error in running R
Student 4 months ago, asked a question with at least 3 up-votes. For Definition and formula of methylation heterogeneity
Popular Question 4 months ago, created a question with more than 1,000 views. For fastq-dump split-spot and skip-technical
Popular Question 4 months ago, created a question with more than 1,000 views. For Gallery: Computational tools for DNA methylation
Popular Question 4 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
Popular Question 4 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
Popular Question 4 months ago, created a question with more than 1,000 views. For R: heatmap for triangular matrix
Appreciated 5 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 5 months ago, created a question with more than 1,000 views. For Protocol To Downlad TCGA Data From GDC
Popular Question 5 months ago, created a question with more than 1,000 views. For R: heatmap for triangular matrix
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Protocol To Downlad TCGA Data From GDC
Appreciated 7 months ago, created a post with more than 5 votes. For A: What is a typical workflow to correlate methylation and expression data?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: error in running R
Good Answer 8 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?
Appreciated 8 months ago, created a post with more than 5 votes. For A: What is a typical workflow to correlate methylation and expression data?
Librarian 8 months ago, created a post with more than 10 bookmarks. For Handbook(s) for Bioinformatics Ninjas
Librarian 8 months ago, created a post with more than 10 bookmarks. For Handbook(s) for Bioinformatics Ninjas
Prophet 9 months ago, created a post with more than 20 followers. For Good Habit for Bioinformatics Analyst or Scientist
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: error in running R
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: error in running R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1557 users visited in the last hour