User: Chen

gravatar for Chen
Chen590
Reputation:
590
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Website:
https://chensunx.githu...
Last seen:
1 day, 15 hours ago
Joined:
5 years, 6 months ago
Email:
b********@gmail.com

Computer Science PhD @ Penn State

Applied Researcher @ Linkedin / Microsoft

Fan of Istvan Albert 

Research Area: Bioinformatics, Algorithms, Machine Learning

Posts by Chen

<prev • 85 results • page 1 of 9 • next >
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Comment: C: What do these 10X Genomics sequencing metrics mean?
... On page 7, Table 1 of this paper: https://www.biorxiv.org/content/early/2017/11/10/217869. Thanks! ...
written 5 days ago by Chen590
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What do these 10X Genomics sequencing metrics mean?
... Some papers report their 10X Genomics barcoded short-reads dataset summary metrics. I can not find the meaning of some metrics on 10X Genomics website. 1. Mean Barcode Richness 2. Mean Barcode Size What does Barcode Richness and Barcode Size mean here? I can only find this: https://support.10xgen ...
10x barcode 10x sequencing 10x genomics written 7 days ago by Chen590
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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 months ago by Chen590
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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 months ago by Chen590
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Comment: C: Which mapping tool takes read quality score into account
... thanks, I will try to dig deeper. ...
written 4 months ago by Chen590
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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 4 months ago by Chen590
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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 4 months ago by Chen590 • updated 4 months ago by h.mon10k
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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 8 months ago by Chen590
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Comment: C: Does jellyfish 2 support kmer size > 31
... Thanks again for your kind help. ...
written 9 months ago by Chen590
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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 9 months ago by Chen590

Latest awards to Chen

Popular Question 11 weeks ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to find the self aligned repeat region in human genome
Student 11 weeks ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 3 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Epic Question 8 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 8 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 8 months ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Scholar 8 months ago, created an answer that has been accepted. For A: Can I get SNP information by individual from dbSNP
Epic Question 17 months ago, created a question with more than 10,000 views. For Which Bioinformatics Tools Are Written In Python
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Epic Question 18 months ago, created a question with more than 10,000 views. For How To Sort Sam File
Popular Question 20 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 21 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Appreciated 22 months ago, created a post with more than 5 votes. 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
Good Question 23 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Good Question 2.2 years ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Great Question 2.2 years ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Popular Question 2.3 years ago, created a question with more than 1,000 views. For How To Find The Most Frequent Allel Snp In Vcf File
Student 2.4 years ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python

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