User: Chen Sun

gravatar for Chen Sun
Chen Sun390
Reputation:
390
Status:
Trusted
Location:
United States
Website:
http://chensunx.github...
Last seen:
2 days, 5 hours ago
Joined:
4 years, 8 months ago
Email:
b********@gmail.com

Computer Science Ph.D. student @ Penn State, with research direction computational biology.

Fan of Istvan Albert.

Personal Website

Posts by Chen Sun

<prev • 74 results • page 1 of 8 • next >
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Does jellyfish 2 support kmer size > 31
... In Jellyfish's original paper(Marcais et al, Bioinformatics 2011), it says that "counting kmers up to 31 bases in length". But on the other hand, in other papers such as KMC2 (Deorowicz et al, Bioinformatics 2015), Jellyfish2 is used to count kmer size = 55. So does Jellyfish support k > 31 no ...
jellyfish kmer kmer counting written 2 days ago by Chen Sun390
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Who is in charge of updating VCF format?
... Variant Call Format (VCF) is in its 4.3 version now. Who is in charge of updating its format standard? ...
vcf written 21 days ago by Chen Sun390 • updated 21 days ago by Pierre Lindenbaum91k
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130
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In GATK, SNPs and INDELs are called separately or together?
... In GATK, SNPs and INDELs are called separately (i.e. they are using different statistical models and different features) or they are called together(in one round with the same statistical model and features). Thanks. ...
indel gatk variant snp written 28 days ago by Chen Sun390 • updated 27 days ago by WouterDeCoster14k
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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 6 weeks ago by Chen Sun390
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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 7 months ago by Chen Sun390
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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 7 months ago by Chen Sun390
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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 7 months ago by Chen Sun390 • updated 7 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 10 months ago by Chen Sun390
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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 10 months ago by Chen Sun390
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Comment: C: Fast way to convert from .SRA files to .Fastq
... Thanks, this idea is very useful!! ...
written 10 months ago by Chen Sun390

Latest awards to Chen Sun

Epic Question 7 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Epic Question 7 months ago, created a question with more than 10,000 views. For How To Sort Sam File
Popular Question 10 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 10 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 12 months ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 12 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 13 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Good Question 16 months ago, asked a question that was upvoted at least 5 times. 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
Great Question 17 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 18 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Student 19 months ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Appreciated 23 months ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Great Question 23 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 23 months ago, created a question with more than 1,000 views. For What'S Easy Framework For Writing Gui Tools In Bioinformatics
Scholar 2.3 years ago, created an answer that has been accepted. For A: Can I get SNP information by individual from dbSNP
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Which Bioinformatics Tools Are Written In Python

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