User: Chen

gravatar for Chen
Chen470
Reputation:
470
Status:
Trusted
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Website:
https://chensunx.githu...
Last seen:
1 week ago
Joined:
4 years, 10 months ago
Email:
b********@gmail.com

Computer Science PhD student @ Penn State

Software Engineer Intern @ Linkedin

Fan of Istvan Albert 

Research Area: Computational Biology, Big Data, Algorithms and Data Structures

Posts by Chen

<prev • 78 results • page 1 of 8 • next >
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Answer: A: How to run local BLAST (Standalone NCBI BLAST+) with Python?
... My solution is to not use biopython, but directly use python function `subprocess`: simply using ``` subprocess.call(command, shell=True) ```, where `command` is any `blast` command you want to run locally. Hope it helps. ...
written 26 days ago by Chen470
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Comment: C: Does jellyfish 2 support kmer size > 31
... Thanks again for your kind help. ...
written 4 weeks ago by Chen470
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Answer: A: Does jellyfish 2 support kmer size > 31
... I will answer this question by myself. I did some test on kmers greater than 31, and at least for the test dataset, the current version of jellyfish does support kmer length > 31. ...
written 4 weeks ago by Chen470
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Comment: C: Correct Way To Parse A Fasta File In Python
... Very useful answer from **7** years ago! FYI, in current version of biopython(1.69), `fasta.seq.tostring()` is obsolete, use `str(fasta.seq)` instead. ...
written 4 weeks ago by Chen470
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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 9 weeks ago by Chen470
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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 12 weeks ago by Chen470 • updated 12 weeks ago by Pierre Lindenbaum94k
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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 3 months ago by Chen470 • updated 3 months ago by WouterDeCoster17k
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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 3 months ago by Chen470
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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 9 months ago by Chen470
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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 9 months ago by Chen470

Latest awards to Chen

Popular Question 13 days ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Scholar 26 days ago, created an answer that has been accepted. For A: Can I get SNP information by individual from dbSNP
Epic Question 9 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Epic Question 10 months ago, created a question with more than 10,000 views. For How To Sort Sam File
Popular Question 12 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 12 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 14 months ago, created a post with more than 5 votes. 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
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Popular Question 19 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 19 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 20 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Student 21 months ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Great Question 2.1 years ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 2.1 years ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 2.1 years ago, created a question with more than 1,000 views. For What'S Easy Framework For Writing Gui Tools In Bioinformatics

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