User: Benm

gravatar for Benm
Benm710
Reputation:
710
Status:
Trusted
Location:
Website:
http://benmfeng.wordpr...
Last seen:
7 years, 3 months ago
Joined:
8 years, 2 months ago
Email:
1***@biostars.org

I come from Nuclear Physics background, and I like most is Nuclear Astrophysics, the second is bioinformatics and algorithm. I was working in one of the biggest genomics center years ago, and now I am the bioinformatics chief of a plant genome project. I'd like to share with and learn from others, because here there are a lot of amazing experts.

Posts by Benm

<prev • 39 results • page 1 of 4 • next >
0
votes
2
answers
4.0k
views
2
answers
Answer: A: Perl Pattern Matching Compare 2 Strings
... perl -e 'my $a="ccgctaccgcgatac";$b="ccgatacgcatcacata";foreach (my $i=0;$i<length($a)-3;$i+=1){my $c=substr($a,$i,3);if ($b=~/$c/){print "$cn";}}' if you need non-redundant elements: perl -e 'my $a="ccgctaccgcgatac";$b="ccgatacgcatcacata";foreach (my $i=0;$i<length($a)-3;$i+=1){my $c=substr($ ...
written 7.5 years ago by Benm710
0
votes
2
answers
1.8k
views
2
answers
Comment: C: Chromosome Translocations Simulation
... you can look for the details from the README: http://sourceforge.net/projects/simulateseq/files/0.2.2/ or just run the command: perl simulateSeq.pl --Example that would give you some example in order to understand it well. And your requirements can be set by " Mutation parameters ", such ...
written 7.5 years ago by Benm710
1
vote
2
answers
1.8k
views
2
answers
Answer: A: Chromosome Translocations Simulation
... Maybe this script of mine - simulateSeq.pl would help you. ...
written 7.5 years ago by Benm710
8
votes
1
answer
14k
views
1
answers
Answer: A: How Mapq In Bwa Is Calculated?
... They come from the same formula. In MAQ: If the mapping quality of a read alignment is $mQ, the probability $me that the alignment is wrong can be calculated with: $me = 10 ** (-$mQ / 10.0); BWA is in SAM format, you can find the MAPQ definition in SAMtools's manuals, The manual i ...
written 7.5 years ago by Benm710
2
votes
7
answers
6.7k
views
7
answers
Answer: A: Compare Two Fasta Files By Headers
... It can be more shorter if the header is case sensitive: awk '/^>/{if (a[$1]>=1){print $1}a[$1]++}' file1 file2 ...
written 8.0 years ago by Benm710
6
votes
2
answers
4.2k
views
2
answers
Answer: A: Genome Assembly Using 2 Insert Size Libraries
... In you stat. info, the situation using both libraries has a double times n50 larger than using only one library, and the contigs number decreased, it seems good performance. Genome assembly , there would be a saturation value of coverage for each libraries, when you try to calculate the n50, whole ...
written 8.0 years ago by Benm710
0
votes
15
answers
7.5k
views
15
answers
Comment: C: Best Language For Introductory Programming Course From Within An Introduction Co
... thank you Michael ...
written 8.0 years ago by Benm710
0
votes
15
answers
7.5k
views
15
answers
Comment: C: Best Language For Introductory Programming Course From Within An Introduction Co
... I can share them with dropbox, do you have dropbox account? ...
written 8.0 years ago by Benm710
2
votes
15
answers
7.5k
views
15
answers
Answer: A: Best Language For Introductory Programming Course From Within An Introduction Co
... I also think PERL, Python, R are the most useful language for bioinformatics, they are easy to study, and they have powerful modules and packages such as: CPAN, CRAN, BioPerl, BioPython(numpy, scipy), so that you can flexibly use them to deal with your tons of biological data. For Learning bioinform ...
written 8.0 years ago by Benm710
1
vote
3
answers
3.4k
views
3
answers
Answer: A: How Can I Align My 454 Reads To A Reference Sequence And Generate A Recruitment
... You can use gsMapper(Newbler v2.5.3, it is not open source software) to align your 454 (sff) reads to reference sequence. But I don't find the suitable software to do 'recruitment plot', I don't know if the CAMERA 1.3.2 could help you, I think you can make it with R using the alignment infor. from ...
written 8.0 years ago by Benm710

Latest awards to Benm

Autobiographer 7.2 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: How Mapq In Bwa Is Calculated?
Good Answer 7.5 years ago, created an answer that was upvoted at least 5 times. For A: How Mapq In Bwa Is Calculated?
Appreciated 7.5 years ago, created a post with more than 5 votes. For A: How Mapq In Bwa Is Calculated?
Good Answer 8.0 years ago, created an answer that was upvoted at least 5 times. For A: Genome Assembly Using 2 Insert Size Libraries
Appreciated 8.0 years ago, created a post with more than 5 votes. For A: Genome Assembly Using 2 Insert Size Libraries
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: Genome Assembly Using 2 Insert Size Libraries
Appreciated 8.0 years ago, created a post with more than 5 votes. For A: Comparison Of Soap And Bwa
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: Comparison Of Soap And Bwa
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: How To Calculate Differential Gene Expression In Rnaseq Experiments?
Appreciated 8.0 years ago, created a post with more than 5 votes. For A: How To Calculate Differential Gene Expression In Rnaseq Experiments?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: A Question About Hybrid Assembly
Good Answer 8.1 years ago, created an answer that was upvoted at least 5 times. For A: A Question About Hybrid Assembly
Appreciated 8.1 years ago, created a post with more than 5 votes. For A: A Question About Hybrid Assembly
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Is Gap Closing Mandatory Process For Soapdenovo Assembly?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: Soapdenovo Assembly Quality Assessment
Teacher 8.2 years ago, created an answer with at least 3 up-votes. For A: What Is The Most Memory-Efficient De Novo Assembler?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1185 users visited in the last hour