User: Johan

gravatar for Johan
Johan770
Reputation:
770
Status:
Trusted
Location:
Sweden
Last seen:
1 month, 3 weeks ago
Joined:
6 years, 4 months ago
Email:
j****@uppsala-bioinformatics.se

Posts by Johan

<prev • 71 results • page 1 of 8 • next >
0
votes
0
answers
256
views
0
answers
Job: System developer at the Swedish National Genomics Infrastructure, SciLifeLab
... System developer at the NGI-Uppsala SNP&SEQ Technology Platform at the Department of Medical Sciences As a part of the National Genomics Infrastructure (NGI) at the Science for Life Laboratory (SciLifeLab, https://www.scilifelab.se), the SNP&SEQ Technology Platform in Uppsala provides SNP-ge ...
sequencing software development genomics job written 3 months ago by Johan770
1
vote
0
answers
1.7k
views
0
answers
Job: Two system developers at the SNP&SEQ technology platform, Uppsala University, Sweden
... Come and join the team at the SNP&SEQ technology platform! We are currently looking for two system developers to help us build the tools for running one of Europe's largest sequencing centers. We work with the latest technology in a cross-disciplinary team to solve exciting problems in the genom ...
system developer jobs job written 3.6 years ago by Johan770
1
vote
0
answers
987
views
0
answers
Job: Two bioinformaticians at the SNP&SEQ technology platform, Uppsala University, Sweden
... Would you like to work in one of the most rapidly growing application areas in the world? As a bioinformatician at the SNP&SEQ technology platform you will work alongside researchers and system developers in a dynamic and creative atmosphere at one of Europe’s largest sequencing centers. You wil ...
bioinformatian jobs job written 3.6 years ago by Johan770 • updated 3.6 years ago by Istvan Albert ♦♦ 77k
1
vote
1
answer
2.2k
views
1
answers
Answer: A: Cummerbund Help
... You can set the directory to read from by: cuff <- readCufflinks(dir="/path/to/your/data") However, if I'm not mistaken cummeRbund should be used to read cuffdiff results, i.ex. results from differential expression studies, which means that normally you would have all you output data in one pl ...
written 4.3 years ago by Johan770
5
votes
16
answers
14k
views
16
answers
Answer: A: Which Bioinformatic Friendly Pipeline Building Framework?
... I've been working with Queue for about a year and a half now, and have it deployed in production at our core facility. I find that it strikes a good balance between expressiveness and simplicity. It has good cluster support, will of course play really nicely with all the GATK tools and is easy to ex ...
written 4.4 years ago by Johan770
1
vote
1
answer
1.4k
views
1
answers
Answer: A: Large Data Set Analysis With Cuffdiff
... Does each sample represent a unique condition? If they are really representatives of different groups you should use the: --labels flag and compare the conditions rather than compare all samples vs. all other samples. Your command line should end up looking something like this: cuffdiff --labels C ...
written 4.4 years ago by Johan770
1
vote
1
answer
3.1k
views
1
answers
Answer: A: Qscript Example For Pipelining Gatk With Queue
... I've been working some with QScripts, in our pipeline project called Piper. The code is available here on github: https://github.com/johandahlberg/piper If you want to start off with some simple example I'd recommend looking at MergeBamsBySample. However, there are some more advanced examples in th ...
written 4.7 years ago by Johan770
0
votes
1
answer
7.8k
views
1
answers
Comment: C: Cuffdiff Command Line For Labels And Replicates
... You are right, I just finished experimenting with this myself before seeing your comment. I added it as a answer below, for future reference. ...
written 5.0 years ago by Johan770
2
votes
1
answer
7.8k
views
1
answers
Answer: A: Cuffdiff Command Line For Labels And Replicates
... I did some experimentation of my own, and just as @Fabio Marroni suggests in his comment to my question the correct way to do it is alternative 1: cuffdiff <other options> --labels conditionA,conditionB <annotations file> sample1.bam,sample2.bam sample3.bam,sample4.bam ...
written 5.0 years ago by Johan770
5
votes
1
answer
7.8k
views
1
answer
Cuffdiff Command Line For Labels And Replicates
... I've been trying to figure out how to setup the cuffdiff command line if one wants both labels and replicates, but I think that the manual could have been more specific on this point. Should there be one label per condition of one per input file. To exemplify: Assume that I have two conditions A a ...
cuffdiff written 5.0 years ago by Johan770

Latest awards to Johan

Great Question 3 months ago, created a question with more than 5,000 views. For Difference Between Picards Mergebamalignment And Mergesamfiles
Great Question 6 months ago, created a question with more than 5,000 views. For Ribosomal Intervals For Collectrnaseqmetrics
Popular Question 8 months ago, created a question with more than 1,000 views. For Samlocusiterator Skips Every Second Locus
Popular Question 13 months ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Linear Regression Of Interacting Genotypes In Java
Great Question 19 months ago, created a question with more than 5,000 views. For Cuffdiff Command Line For Labels And Replicates
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Linear Regression Of Interacting Genotypes In Java
Popular Question 24 months ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Difference Between Picards Mergebamalignment And Mergesamfiles
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Which Bioinformatic Friendly Pipeline Building Framework?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Two system developers at the SNP&SEQ technology platform, Uppsala University, Sweden
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Student 3.6 years ago, asked a question with at least 3 up-votes. For Ribosomal Intervals For Collectrnaseqmetrics
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Transcript Assembly In Dense Genome Using Cufflinks
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Ribosomal Intervals For Collectrnaseqmetrics
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Tophat - Expectancy Of Properly Paired Reads?
Voter 4.2 years ago, voted more than 100 times.
Supporter 4.2 years ago, voted at least 25 times.
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Linear Regression Of Interacting Genotypes In Java
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Visualizing The Outputs Of Gatk/Depthofcoverage
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Vcf File With Variants And Genotypes For A "Single Individual"
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Microarray Class Prediction - For Continuous Data?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1175 users visited in the last hour