Moderator: JC

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JC6.2k
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Mexico
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http://about.me/jcabal...
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Computational Biologist

Posts by JC

<prev • 545 results • page 1 of 55 • next >
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Comment: C: what to do when adjusted p-values are not acceptable in RNASeq?
... 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 JC6.2k
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Tool: Databiology CIAO: Develop applications quickly and easily. Increase your productivity and enable portability with our full application development environment.
... 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 ...
bioinformatic development apps framework tool written 21 days ago by JC6.2k
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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 JC6.2k
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Tool: Databiology Lab: 100s of bioinformatics apps and public data sets available with free compute and storage
... 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 ...
bioinformatics platform tool data written 4 weeks ago by JC6.2k
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Answer: A: reference-guided genome assembly: stretches of Ns
... 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 JC6.2k
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Answer: A: I want to know about the actual function of Bowtie?
... 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 JC6.2k
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Answer: A: Opinion: Another MSA or Pairwise alignment tool would be useful in bioinformatic
... 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 JC6.2k
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Comment: C: What is first publication/mention of term RNA-seq
... Which one do you mean? ...
written 7 months ago by JC6.2k
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Comment: C: What is first publication/mention of term RNA-seq
... Yes. The method is RNAseq basically. So, this is the first RNASEQ paper ever made? ...
written 7 months ago by JC6.2k
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Comment: C: Number of contigs does not match number in count matrix --- de novo assembly
... are you counting genes or transcripts? ...
written 14 months ago by JC6.2k

Latest awards to JC

Commentator 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
Scholar 7 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Solid Data From Sra
Scholar 7 months ago, 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 10 months ago, created an answer with at least 3 up-votes. For A: Solid Data From Sra
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
Scholar 18 months ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 19 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 21 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
Scholar 2.1 years ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Use Tabix With A List Of Regions
Teacher 2.2 years 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
Scholar 2.2 years ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 2.2 years 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
Scholar 2.2 years ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Optimal Scaling Of Digital Transcriptomes
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Programming Challenge - Synthetic Whole Genome Vcf
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Macosx For Bioinformatics?
Teacher 2.8 years 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
Scholar 2.8 years ago, created an answer that has been accepted. For A: Best way to remove contaminants to get nuclear genome
Teacher 2.8 years 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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