Difference between revisions of "HLab:Main"
From CCGB
(→Computing at BX) |
|||
| (27 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | [[File:HardisonLabPhoto2007.jpg|thumb|Lab mates]] | ||
| + | Hi, the is the wiki "HOME" for Hardison Lab. Everyone is welcome to edit it. '''This contains our laboratory protocols and other resources.''' | ||
| − | [[ | + | If you are a visitor and interested in the lab projects, please go this way to the [http://www.bx.psu.edu/~ross/ Hardison lab homepage.] <br />If you are a member of this lab, you can use your login name and password to access our database: [[HLab:HardisonData]] or view [[hlab:Hardison_Lab_Meetings|meeting notes.]] |
| − | + | ==Resources== | |
| − | + | ===Servers=== | |
| − | + | [http://cladimo.bx.psu.edu/ CladiMo] search tool for conserved motifs. | |
| − | + | [http://www.bx.psu.edu/~dcking/mafgraph/mafbrowser.html MAF browser] - an interactive Flash tool for exploring MAF alignment files. | |
| − | [http:// | + | [http://main.genome-browser.bx.psu.edu BX Browser] - a mirror of the UCSC Genome Browser with tracks from Hardison lab added |
| − | [ | + | [https://mery.genome-browser.bx.psu.edu Mery Browser] - login required, a mirror like above with unpublished data |
| − | == | + | ===Seminars=== |
| + | [http://csg.psu.edu/seminars/weekly-genomics-seminar Weekly Genomics Seminar schedule] | ||
===Laboratory Protocols=== | ===Laboratory Protocols=== | ||
| Line 40: | Line 43: | ||
*[[hlab:ChIP]] | *[[hlab:ChIP]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
=== Methods === | === Methods === | ||
Various techniques and approaches get re-invented frequently. This section is devoted to keep that from happening. | Various techniques and approaches get re-invented frequently. This section is devoted to keep that from happening. | ||
| − | *Illumina post processing [[Hlab:steps]] | + | *Illumina post processing [[Hlab:steps|steps]] |
| − | *Workflows for processing data [[Hlab:workflows]] | + | *Workflows for processing data [[Hlab:workflows|workflows]] |
| + | *Quality metrics [[Hlab:qualitymetrics|description]] | ||
| + | *Using [[Hlab:gedi|GEDI maps]] | ||
| + | *File sharing or transfer [[Hlab:fileshare|methods]] login required | ||
| + | *R [[Hlab:rscripts|scripts]] | ||
| + | *Perl [[Hlab:perlscripts|scripts]] | ||
| − | ==== | + | === Publications and Posters === |
| − | + | *[[media:GenomeInformatics2013Giardine.pdf|Workflow poster]] for Genome Informatics 2013 | |
| − | *[[ | + | *[[Hlab:HardisonData]] login required |
| − | + | *[[Hlab:Hardison_Lab_Meetings|lab meetings]] login required | |
| − | *[[ | ||
=== Computing at BX=== | === Computing at BX=== | ||
| − | [[BX:Main]], [http://ganglia.bx.psu.edu/ Ganglia] | + | *[[BX:Main]], [http://ganglia.bx.psu.edu/ Ganglia] |
=== Wiki === | === Wiki === | ||
*[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wikipedia Cheatsheet] | *[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Wikipedia Cheatsheet] | ||
| − | |||
| − | |||
| − | |||
---- | ---- | ||
Or, if you just want to have some fun here, well, usually we are not joking during work, but check this: [[For Fun]] | Or, if you just want to have some fun here, well, usually we are not joking during work, but check this: [[For Fun]] | ||
Latest revision as of 09:24, 2 April 2015
Hi, the is the wiki "HOME" for Hardison Lab. Everyone is welcome to edit it. This contains our laboratory protocols and other resources.
If you are a visitor and interested in the lab projects, please go this way to the Hardison lab homepage.
If you are a member of this lab, you can use your login name and password to access our database: HLab:HardisonData or view meeting notes.
Contents
Resources
Servers
CladiMo search tool for conserved motifs.
MAF browser - an interactive Flash tool for exploring MAF alignment files.
BX Browser - a mirror of the UCSC Genome Browser with tracks from Hardison lab added
Mery Browser - login required, a mirror like above with unpublished data
Seminars
Weekly Genomics Seminar schedule
Laboratory Protocols
Methods
Various techniques and approaches get re-invented frequently. This section is devoted to keep that from happening.
- Illumina post processing steps
- Workflows for processing data workflows
- Quality metrics description
- Using GEDI maps
- File sharing or transfer methods login required
- R scripts
- Perl scripts
Publications and Posters
- Workflow poster for Genome Informatics 2013
- Hlab:HardisonData login required
- lab meetings login required
Computing at BX
Wiki
Or, if you just want to have some fun here, well, usually we are not joking during work, but check this: For Fun
