User: Chen Sun

gravatar for Chen Sun
Chen Sun380
Reputation:
380
Status:
Trusted
Location:
United States
Last seen:
3 days, 5 hours ago
Joined:
4 years, 6 months ago
Email:
b********@gmail.com

Ph.D. Candidate from Computer Science and Engineering Department, The Pennsylvania State University, with research direction computational biology.

Fan of Istvan Albert (of course, who isn't?).

Posts by Chen Sun

<prev • 71 results • page 1 of 8 • next >
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Comment: C: where to download blat command tool for windows?
... Thank you for the answer. This is exactly the one I want!! ...
written 15 days ago by Chen Sun380
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Comment: C: Can FM Index be built in linear time?
... the running time analysis actually matters if we want to iteratively build FM-index (e.g. build FM-index 100 times by integrating genetic variants in each iteration) or dynamically build FM index ...
written 6 months ago by Chen Sun380
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Comment: C: Can FM Index be built in linear time?
... I suppose BWA is also based on O(nlgn) algorithm, as analyzed in Li et al., 2014 ...
written 6 months ago by Chen Sun380
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Can FM Index be built in linear time?
... In short, my question is: 1. what is the running time of building FM-Index, is it linear in the sense of reference genome? I was told that FM-Index can be built in linear time, i.e. O(n), where n is the length of reference genome. But I actually can not find the paper describing it. The paper cite ...
bowtie2 alignment bwa bowtie fm-index written 6 months ago by Chen Sun380 • updated 6 months ago by lh328k
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Comment: C: Is there a Faster tool to convert from .SRA files to .Fastq ?
... it's next generation sequencing data, hiseq raw reads for genome ...
written 9 months ago by Chen Sun380
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Comment: C: How To Split A Bam File By Chromosome
... A solution would be converting bam to fastq file, then use the fastq to map to specific chromosome ...
written 9 months ago by Chen Sun380
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Comment: C: Fast way to convert from .SRA files to .Fastq
... Thanks, this idea is very useful!! ...
written 9 months ago by Chen Sun380
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Comment: C: Fast way to convert from .SRA files to .Fastq
... It is hp SAS disk. ...
written 9 months ago by Chen Sun380
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Is there a Faster tool to convert from .SRA files to .Fastq ?
... I download a SRA file from NCBI, with 166G size. Then I use fastq-dump -I --split-files ./File.sra to convert it to fastq file on a server with 1Tb memory and 10K RPM disk. With four hours it only generates 400M fastq file, it seems that convering the file will take forever. To be precise, its c ...
ncbi sra fastq written 9 months ago by Chen Sun380
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Comment: C: where to download blat command tool for windows?
... I write tools for others, not myself, and most users from biology labs are using windows. ...
written 9 months ago by Chen Sun380

Latest awards to Chen Sun

Epic Question 6 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Epic Question 6 months ago, created a question with more than 10,000 views. For How To Sort Sam File
Popular Question 8 months ago, created a question with more than 1,000 views. For Delly: how does delly decide whether a SV is imprecise or precise
Great Question 9 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 11 months ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 11 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Great Question 16 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 16 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Student 18 months ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Appreciated 21 months ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Great Question 21 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 22 months ago, created a question with more than 1,000 views. For What'S Easy Framework For Writing Gui Tools In Bioinformatics
Scholar 2.2 years ago, created an answer that has been accepted. For A: Can I get SNP information by individual from dbSNP
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Which Bioinformatics Tools Are Written In Python

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