User: Yu

gravatar for Yu
Yu100
Reputation:
100
Status:
Trusted
Location:
China
Last seen:
17 hours ago
Joined:
6 years, 11 months ago
Email:
y*******@gmail.com

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Posts by Yu

<prev • 27 results • page 1 of 3 • next >
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Comment: C: sliding windows with or without overlap?
... Thank you. Sliding windows may provide more resolution. ...
written 21 months ago by Yu100
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Comment: C: Confused with Ensembl Exon ID, How to understand them?
... first "1" on every column is name of the chromosome ( chromosome 1 ). exon_version: The stable identifier version for this exon. you can find gtf format detail from: ftp://ftp.ensembl.org/pub/release-81/gtf/homo_sapiens/README ...
written 21 months ago by Yu100
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sliding windows with or without overlap?
... Dear all, I am confused about sliding window method, we often using this method to analysis ChIP-seq data or Copy number variation(CNV). Sliding windows w/o overlap is divided genome into several equal segments, it often used in CNV analysis. Sliding windows w/ overlap is like [moving average in s ...
chip-seq sliding windows cnv written 3.0 years ago by Yu100 • updated 3.0 years ago by Ibrahim Tanyalcin930
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Comment: C: question about macs2 --broad-cutoff
... Thanks a lot ! Using `q-value` can filer out `-log10(qvalue) <2` peaks successfully. ...
written 3.0 years ago by Yu100
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Comment: C: question about macs2 --broad-cutoff
... I think you didn't get my point. My question is how to set `-q` `-p` or `--broad-cutoff` to filter out `-log10(qvalue) <2` in my post example above. My post is ask why my result didn't filter out `-log10(qvalue) <2`, the options used are in the result file. Thanks for your support. ...
written 3.0 years ago by Yu100
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Comment: C: question about macs2 --broad-cutoff
... Thanks. Can you give me some example, how to set the q-value, p-value and broad-cutoff, then I can filter out -log10(qvalue) <2 in my result list? ...
written 3.0 years ago by Yu100
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question about macs2 --broad-cutoff
... Dear all, I am confused with the --broad-cutoff option in macs2. In the manual, it said that --broad-cutoff is cutoff for broad region. This option is not available unless --broad is set. If -p is set, this is a pvalue cutoff, otherwise, it's a qvalue cutoff. DEFAULT: 0.1 If I understand it correc ...
macs2 broadpeak broad-cutoff chip-seq written 3.0 years ago by Yu100 • updated 3.0 years ago by ivivek_ngs4.7k
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Comment: C: Is Any Database Provide Human Genes' Conservation Scores ?
... Hi,  For each gene, the gene transcription start site and transcription terminal site were defined by the ensembl annotation file(gtf). So I only calculate the mean value between transcription start site and transcription terminal site. If memory serves me right, within the scope of my research, I ...
written 3.4 years ago by Yu100
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Comment: C: Detect circular RNA using RNA-seq
... Hi,  just a hint here. I download the latest version of segemehl (0.2.0), try the same command as David's. However, the testrealign.x program only give me two output files, splicesites.bed and transrealigned.bed, the program doesn't provide circular.bed file. I read the manual and find that I can de ...
written 3.6 years ago by Yu100
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Comment: C: Is Any Database Provide Human Genes' Conservation Scores ?
... Hi Jeff, Sorry for the delay in replying. I downloaded the UCSC conservation scores (primates phastCons46way) and calculate the mean value of each gene.  @Alex Reynolds also provide you a good way to calculate the gene conservation score. https://www.biostars.org/p/150152/ ...
written 3.6 years ago by Yu100

Latest awards to Yu

Great Question 5 months ago, created a question with more than 5,000 views. For Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl
Great Question 10 months ago, created a question with more than 5,000 views. For Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl
Popular Question 20 months ago, created a question with more than 1,000 views. For Confused with Ensembl Exon ID, How to understand them?
Popular Question 23 months ago, created a question with more than 1,000 views. For Is Any Database Provide Human Genes' Conservation Scores ?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Is Any Database Provide Human Genes' Conservation Scores ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Is Any Database Provide Human Genes' Conservation Scores ?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl
Supporter 3.4 years ago, voted at least 25 times.
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Is Any Database Provide Human Genes' Conservation Scores ?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl
Student 5.6 years ago, asked a question with at least 3 up-votes. For Is Any Database Provide Human Genes' Conservation Scores ?

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