User: Chen

gravatar for Chen
Chen560
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560
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Website:
https://chensunx.githu...
Last seen:
2 hours ago
Joined:
5 years, 2 months ago
Email:
b********@gmail.com

Computer Science PhD student @ Penn State

Software Engineer Intern @ Linkedin

Fan of Istvan Albert 

Research Area: Bioinformatics, Algorithms, Machine Learning

Posts by Chen

<prev • 83 results • page 1 of 9 • next >
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Comment: C: Bioinformatics "Cheat Sheet"
... **Warning:** there is a small difference between hg19 and GRCh37 that make a significant influence in the downstream analysis: in GRCh37, the chromosome name is 1,2,3,4,5,6,7,8,9,..., X, Y in hg19, the chromosome name is chr1, chr2, chr3, chr4, ..., chrX, chrY So the mapping results to hg19 canno ...
written 4 days ago by Chen560
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Answer: A: What Are The Most Common Stupid Mistakes In Bioinformatics?
... Since no one mentioned. The uppercase/lowercase error. Sometimes, you need to distinguish between "atgc" and "ATGC". But in most cases, they mean the same thing. So always convert any string you met to uppercase if you do not need to distinguish. I feel spending my whole Ph.D. debugging this. Hop ...
written 4 days ago by Chen560
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Comment: C: Which mapping tool takes read quality score into account
... thanks, I will try to dig deeper. ...
written 11 days ago by Chen560
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Comment: C: CuteVariant : A GUI to filter VCF file
... Can I ask which platform you want to support? win, mac or linux? ...
written 11 days ago by Chen560
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Which mapping tool takes read quality score into account
... Read quality score is an important information, if the quality score for certain position is very low, then the nucleotide at that position might be a sequencing error. So mapping tools might can not directly use that nucleotide to map, but try to solve the sequencing error issue. From the paper I ...
bowtie2 mapping bwa quality score written 12 days ago by Chen560 • updated 11 days ago by h.mon8.7k
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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 4 months ago by Chen560
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Comment: C: Does jellyfish 2 support kmer size > 31
... Thanks again for your kind help. ...
written 5 months ago by Chen560
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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 5 months ago by Chen560
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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 5 months ago by Chen560
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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 6 months ago by Chen560

Latest awards to Chen

Epic Question 4 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 4 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Popular Question 4 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Scholar 4 months ago, created an answer that has been accepted. For A: Can I get SNP information by individual from dbSNP
Epic Question 13 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Epic Question 14 months ago, created a question with more than 10,000 views. For How To Sort Sam File
Popular Question 16 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 17 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 18 months ago, created a post with more than 5 votes. 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
Good Question 19 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Popular Question 23 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 23 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 24 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Student 2.1 years ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Great Question 2.4 years ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 2.4 years ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 2.4 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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