informatics.fas.harvard.edu

Informatics and Scientific Applications

Informatics and Scientific Applications. Unix Tips and Tricks. ChIP-Seq Workshop – HOXB7. Unix Soup to Nuts. IggyTools – seqprep test process. Back in 1997 I never thought I would see this – Jalview. With it’s own booth. Jim Procter stands proudly (and rightly so) by the custom display for the long lived, widely used and much loved multiple alignment visualization and editing tool. Sample status for the previous month. Genome and Database Repository. Latest paper from Tim Sackton in PLoS Biology.

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Informatics and Scientific Applications | informatics.fas.harvard.edu Reviews

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Informatics and Scientific Applications. Unix Tips and Tricks. ChIP-Seq Workshop – HOXB7. Unix Soup to Nuts. IggyTools – seqprep test process. Back in 1997 I never thought I would see this – Jalview. With it’s own booth. Jim Procter stands proudly (and rightly so) by the custom display for the long lived, widely used and much loved multiple alignment visualization and editing tool. Sample status for the previous month. Genome and Database Repository. Latest paper from Tim Sackton in PLoS Biology.

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Informatics and Scientific Applications | informatics.fas.harvard.edu Reviews

https://informatics.fas.harvard.edu

Informatics and Scientific Applications. Unix Tips and Tricks. ChIP-Seq Workshop – HOXB7. Unix Soup to Nuts. IggyTools – seqprep test process. Back in 1997 I never thought I would see this – Jalview. With it’s own booth. Jim Procter stands proudly (and rightly so) by the custom display for the long lived, widely used and much loved multiple alignment visualization and editing tool. Sample status for the previous month. Genome and Database Repository. Latest paper from Tim Sackton in PLoS Biology.

INTERNAL PAGES

informatics.fas.harvard.edu

1

Basic Unix Workshop - Harvard FAS Informatics

http://informatics.fas.harvard.edu/intro-to-unix-with-an-ngs-slant

Table of Contents ( show. Summary of Commands Covered. 1 Logging in and the command prompt. 4 Command line editing. Listing a subset of files. Sorting a file list. Human readable format for file size. 81 Using an editor. 82 Using the cat command. 83 Using redirect from a command into a file. 9 Looking at File Contents. 91 The head command - beginnings of files. 92 The tail command - ends of files. 93 The less command - scrolling and searching large files. 10 Making Directories - mkdir. Wed 13 January 2016.

2

Cores - Harvard FAS Informatics

http://informatics.fas.harvard.edu/minilims-documentation

FAS Informatics provides software and technology support to the FAS Core Facilities, including the Bauer Sequencing Core, Small Molecule Mass Spectrometry, Protein Mass Spectrometry. Our core sequencing service has two Illumina HiSeqs and a MiSeq. The FAS Informatics group is committed to providing a fast basecalling and QC service for all users of the facility. Beyond this we strongly encourage people to get in contact with us michele clamp@harvard.edu. Helium Liquefaction and Recovery Core. The Small M...

3

Faq - Harvard FAS Informatics

http://informatics.fas.harvard.edu/faq

Below are a number of Frequently Asked Questions. Questions and answers are below, but if you click on the question, more detail may be available. A couple of my fastq.gz files will not decompress, or give errors when I process them. What is wrong? Occasionally, large files become corrupted during download. You can determine whether this has occurred by comparing the checksum. How can I download my sequencing data. What computing resources are available to FAS and HSPH? When aligning paired reads, alignm...

4

Next-Gen Sequencing - Harvard FAS Informatics

http://informatics.fas.harvard.edu/category/next-gen-sequencing

Best Practices for De Novo Transcritome Assembly with Trinity. A best-practices pipeline for de novo transcriptome assembly with Illumina paired-end reads using Trinity. Analyzing public ChIP-seq data for orthologs of genes of interest. An example workflow for identifying orthologs of genes of interest from one organism by analyzing ChIP-seq data from another organism. Metatranscriptome analysis example on Odyssey. An example of preprocessing and analyzing microbiome RNA-seq data on the Odyssey cluster.

5

MiniLIMS Activity - Harvard FAS Informatics

http://informatics.fas.harvard.edu/minilims-lims-activity

Table of Contents ( show. Small Molecule Mass Spec since 2015-03-12. Bauer Sequencing Core since 2015-03-12. Mass Spec Proteomics Core since 2015-03-12. Tue 06 October 2015. Small Molecule Mass Spec since 2015-03-12. Last updated: 9/9/2015 13:34. Bauer Sequencing Core since 2015-03-12. Last updated: 9/9/2015 13:34. Mass Spec Proteomics Core since 2015-03-12. Last updated: 9/9/2015 13:34. Last updated: 9/9/2015 13:34. 2999 Aaron Kitzmiller · Powered by pelican-bootstrap3.

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rc.fas.harvard.edu

FAQ | FAS Research Computing

https://rc.fas.harvard.edu/resources/faq

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). The turnaround time is us...

rc.fas.harvard.edu

Training | FAS Research Computing

https://rc.fas.harvard.edu/training

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). Office Hours: Tips at 12.

rc.fas.harvard.edu

Introduction to Odyssey — Online | FAS Research Computing

https://rc.fas.harvard.edu/training/intro-to-odyssey

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). Step 1: Watch the Video.

rc.fas.harvard.edu

Training | FAS Research Computing

https://rc.fas.harvard.edu/education/training

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). Office Hours: Tips at 12.

rc.fas.harvard.edu

Documentation | FAS Research Computing

https://rc.fas.harvard.edu/resources/documentation

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). View more FAQ pages.

rc.fas.harvard.edu

Training Materials | FAS Research Computing

https://rc.fas.harvard.edu/training/training-materials

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). Page or our Documentation.

rc.fas.harvard.edu

Events Calendar | FAS Research Computing

https://rc.fas.harvard.edu/events

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). August 31, 2016. OpenMPI ...

rc.fas.harvard.edu

Odyssey storage | FAS Research Computing

https://rc.fas.harvard.edu/resources/odyssey-storage

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). 100 GB (Hard Limit).

rc.fas.harvard.edu

Office Hours | FAS Research Computing

https://rc.fas.harvard.edu/training/office-hours-special-topics

HARVARD UNIVERSITY FACULTY OF ARTS and SCIENCES. 8211; Login/Account FAQs. 8211; Slurm/Job FAQs. 8211; Filesystem/Authorization FAQs. 8211; Software FAQs. Harvard Chan School (HCSPH). Odyssey Quick Start Guide. 8211; Convenient SLURM Commands. 8211; What is Fair-Share? 8211; Modules Introduction. 8211; Running Software. 8211; Installing Software Yourself. Introduction to Odyssey & RC Services. Next Steps on Odyssey! Parallel Computing on Odyssey. HCSPH Bioinformatics Core (HBC). Past titles and materials:.

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Informatics and Scientific Applications

Informatics and Scientific Applications. Unix Tips and Tricks. ChIP-Seq Workshop – HOXB7. Unix Soup to Nuts. IggyTools – seqprep test process. Back in 1997 I never thought I would see this – Jalview. With it’s own booth. Jim Procter stands proudly (and rightly so) by the custom display for the long lived, widely used and much loved multiple alignment visualization and editing tool. Sample status for the previous month. Genome and Database Repository. Latest paper from Tim Sackton in PLoS Biology.

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