User: Chen
Chen • 560
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Computer Science PhD student @ Penn State
Software Engineer Intern @ Linkedin
Fan of Istvan Albert
Research Area: Bioinformatics, Algorithms, Machine Learning
Posts by Chen
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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
Chen • 560
2
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73
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73
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... 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
Chen • 560
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0
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116
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... thanks, I will try to dig deeper. ...
written 11 days ago by
Chen • 560
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142
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... Can I ask which platform you want to support? win, mac or linux? ...
written 11 days ago by
Chen • 560
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... 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 ...
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1
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... 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
Chen • 560
0
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2
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279
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... Thanks again for your kind help. ...
written 5 months ago by
Chen • 560
2
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279
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... 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
Chen • 560
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7
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7
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... 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
Chen • 560
11
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2
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... 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 ...
written 6 months ago by
Chen • 560
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4 months ago,
created a question with more than 10,000 views.
For Which Bioinformatics Tools Are Written In Python
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For How To Find The Most Frequent Allel Snp In Vcf File
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Scholar
4 months ago,
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For A: Can I get SNP information by individual from dbSNP
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13 months ago,
created a question with more than 10,000 views.
For Which Bioinformatics Tools Are Written In Python
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13 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
Appreciated
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created a post with more than 5 votes.
For Which Journals Should I Follow If I Write Software And Algorithms In Computational Biology?
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14 months ago,
created a question with more than 10,000 views.
For How To Sort Sam File
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created a question with more than 1,000 views.
For Delly: how does delly decide whether a SV is imprecise or precise
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17 months ago,
created a question with more than 5,000 views.
For Which Bioinformatics Tools Are Written In Python
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17 months ago,
created a question with more than 1,000 views.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
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18 months ago,
created a question with more than 1,000 views.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
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18 months ago,
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For Which Bioinformatics Tools Are Written In Python
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18 months ago,
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For Which Journals Should I Follow If I Write Software And Algorithms In Computational Biology?
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19 months ago,
created a question with more than 1,000 views.
For How To Find The Most Frequent Allel Snp In Vcf File
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19 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
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23 months ago,
asked a question that was upvoted at least 5 times.
For Which Bioinformatics Tools Are Written In Python
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23 months ago,
created a question with more than 1,000 views.
For How To Find The Most Frequent Allel Snp In Vcf File
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23 months ago,
created a question with more than 5,000 views.
For Which Bioinformatics Tools Are Written In Python
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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
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
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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