Moderator: JC
JC ♦ 6.2k
- Reputation:
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- Mexico
- Website:
- http://about.me/jcabal...
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- Last seen:
- 2 days, 2 hours ago
- Joined:
- 5 years, 4 months ago
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Computational Biologist
Posts by JC
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... Cancer is really diverse in gene expression, could be better to analyze your cancer samples individually using the normals as "control", also you probably want to try another package as EdgeR to see if this is something particular in your dataset. ...
written 8 days ago by
JC ♦ 6.2k
2
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223
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... Dear Biostar Community,
We are looking for developers in for a preview testing phase who can create or port their tools (or even pipelines) in Databiology Lab using our CIAO (Continuous Integration Application Onboarding) framework. CIAO allows developers:
- Integrates with your own source or bin ...
written 21 days ago by
JC ♦ 6.2k
0
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1
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274
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Comment:
C: blast query coverage using perl
... extending a little more this;
perl -lane 'if (/^Query/) { $v = "Calculated_q_coverage" } else { $v = $F[2] - $F[1] + 1; } print join "\t", @F, $v;' < test.txt > test_out.txt ...
written 29 days ago by
JC ♦ 6.2k
3
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... Dear Biostar Community,
We are pleased to announce the preview launch of Databiology Lab.
Databiology Lab is a cloud platform for biomedical research such as genomics, proteomics, neuroinformatics and others. In Databiology Lab, users can create, collect store, query, analyze and share biomedical ...
written 4 weeks ago by
JC ♦ 6.2k
0
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2
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305
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... In general, those uncalled regions are created when you have paired-ends reads and regions between pairs are empty (no reads means no coverage), so the assembler is just reporting N's. You can as you said trying to do a de novo assembly and check if those regions are deletions (you can also see that ...
written 5 months ago by
JC ♦ 6.2k
3
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... Bowtie is a set of programs, "bowtie-build" creates the index from a reference genome. After having your index, "bowtie" aligns short sequences (in Fasta or Fastq format) into the index. ...
written 7 months ago by
JC ♦ 6.2k
4
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251
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... If your tool has better performance (speed, sensitivity, accuracy...) definitely will be useful. Also if it's a novel approach. So, my suggestion is to open your code and left the world decide. ...
written 7 months ago by
JC ♦ 6.2k
0
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4
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2.5k
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4
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... Which one do you mean? ...
written 7 months ago by
JC ♦ 6.2k
0
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4
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2.5k
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4
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... Yes. The method is RNAseq basically. So, this is the first RNASEQ paper ever made? ...
written 7 months ago by
JC ♦ 6.2k
0
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464
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... are you counting genes or transcripts? ...
written 14 months ago by
JC ♦ 6.2k
Latest awards to JC
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8 days ago,
created a comment with at least 3 up-votes.
For C: What Should I Use Blat For?
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Programming Challenge - Synthetic Whole Genome Vcf
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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7 months ago,
created an answer that has been accepted.
For A: Best way to remove contaminants to get nuclear genome
Scholar
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created an answer that has been accepted.
For A: How to check whether the mate read is fully mapped or not?
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: Programming Challenge - Synthetic Whole Genome Vcf
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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For A: Best way to remove contaminants to get nuclear genome
Teacher
19 months ago,
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For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
Teacher
21 months ago,
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For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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For A: Best way to remove contaminants to get nuclear genome
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2.2 years ago,
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For A: Use Tabix With A List Of Regions
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2.2 years ago,
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For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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2.2 years ago,
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For A: Best way to remove contaminants to get nuclear genome
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2.2 years ago,
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For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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For Optimal Scaling Of Digital Transcriptomes
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For A: Programming Challenge - Synthetic Whole Genome Vcf
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For A: Macosx For Bioinformatics?
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For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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2.8 years ago,
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For A: Best way to remove contaminants to get nuclear genome
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2.8 years ago,
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For A: What Do The Period . Symbols Mean In The Sequence Record Of A Fastq File
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