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Combined display of all available logs of OpenWetWare. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 18:06, 8 November 2023 Schumer talk contribs created page Schumer lab: Passaging cells (Created page with "refer to the "passaging caudal cells" protocol in the cell culture protocols folder on dropbox")
- 14:05, 8 November 2023 Schumer talk contribs created page Schumer lab: NEB Monarch Tissue HMW DNA extraction (Created page with "[Insert stuff here] -JJ")
- 13:52, 8 November 2023 Schumer talk contribs created page Schumer lab: Changing media (Created page with "In Xiphophorus cell culture, (as of 11/08/23) media is changed on Monday, Wednesday and Friday. Premade complete media aliquots should be stored in the 4 degree fridge in a 50 mL falcon tube. 12 well plates should have a total volume of 2 mL media in each well, while T25 flasks should have a total of 5 mL of media.")
- 15:47, 23 May 2023 Schumer talk contribs created page Schumer lab: Data currently available on Oak (Created page with "==Data currently available on Oak=== We keep an up-to-date log of data currently available on Oak in the following google sheet. If you download any raw data, please make sure to update it! https://docs.google.com/spreadsheets/d/1dUBAmaz2bNa-LppWxFZ7Vymld-jxrDbh-HC_WFjXSzA/edit#gid=89601434")
- 16:38, 22 May 2023 Schumer talk contribs created page Schumer lab: Swordtail Dropbox quick guide (Created page with "==Swordtail Dropbox== Dropbox is home to the most important documents in the lab that aren't raw data. For ease of access, I am also linking some commonly used documents here: *Lab manual *New lab member checklist *Site codes and information *")
- 15:42, 22 May 2023 Schumer talk contribs created page Schumer lab: Shared resources (Created page with "==Introduction== Many people in the lab use the same shared resources and contribute to developing these resources. Resource files such as genome assemblies, annotation files, recombination maps, and files for ancestry inference can all be found in: <span style="font-family:Courier;">/home/groups/schumer/shared_bin/shared_resources ===Current resources map=== This google document describes the most commonly used resources in shared_resources and provides useful info...")
- 15:42, 7 July 2021 Schumer talk contribs created page Schumer lab: Lab member folders (Created page with "==Lab member folders on OAK== You will often want to backup files that are too big to go on the lab directory on Sherlock but you want to keep more permanently than scratch w...")
- 16:54, 15 May 2020 Schumer talk contribs created page Schumer lab:Grad program (Created page with "==Overview== ==First year== ==Quals== ==Reading committee & Defense==")
- 09:16, 10 October 2019 Schumer talk contribs created page Schumer lab: Download data to Sherlock from Admera (Created page with "==Download data with ftp== To download data to Sherlock with ftp, navigate to the directory you would like to download to, and load the ftp module: <span style="font-family:...")
- 16:41, 9 June 2019 Schumer talk contribs created page File:SELAM manual.pdf
- 16:41, 9 June 2019 Schumer talk contribs uploaded File:SELAM manual.pdf
- 15:52, 9 June 2019 Schumer talk contribs created page File:SupernovaAssembly v1.pdf
- 15:52, 9 June 2019 Schumer talk contribs uploaded File:SupernovaAssembly v1.pdf
- 17:09, 14 April 2019 Schumer talk contribs created page Schumer lab: Processed files available on Oak (Created page with " __FORCETOC__ ==Previously generated bam files== Mapped to the X. hellerii genome (GCA_003331165.1_Xiphophorus_hellerii-4.0_genomic.fna) with bwa mem, sorted & deduplicate...")
- 16:57, 14 April 2019 Schumer talk contribs created page File:Common file formats genomics.pdf
- 16:57, 14 April 2019 Schumer talk contribs uploaded File:Common file formats genomics.pdf
- 20:17, 12 April 2019 Schumer talk contribs created page File:Msdoc.pdf
- 20:17, 12 April 2019 Schumer talk contribs uploaded File:Msdoc.pdf
- 12:28, 12 April 2019 Schumer talk contribs created page Schumer lab: Download data to Sherlock from NCBI's SRA (Created page with "==Get and convert data==")
- 17:34, 10 April 2019 Schumer talk contribs created page Schumer lab: Bam file map on Oak (Created page with "==Previously generated bam files== ==Previously generated tsv files==")
- 17:33, 10 April 2019 Schumer talk contribs created page Schumer lab: Raw data map on Oak (Created page with "==Current raw data directories==")
- 17:30, 10 April 2019 Schumer talk contribs created page Schumer lab: Backing up raw data (Created page with "==Back up your raw data on external hard drives or the SRA== '''It is very important to regularly backup your raw data!''' There are two options for backing up your raw fast...")
- 19:30, 7 April 2019 Schumer talk contribs created page Schumer lab: Depositing data on Oak (Created page with "==Introduction== Oak is a large storage resource where we can keep large raw data files and large processed data files. You can link to files on Oak from your local directory...")
- 14:54, 5 April 2019 Schumer talk contribs created page Schumer lab: Useful web programs (Created page with "===Gene prediction=== *[https://www.ebi.ac.uk/Tools/psa/genewise/ genewise] ===Online translation=== *[https://web.expasy.org/translate/ translate cDNA to protein] ===Sequ...")
- 20:09, 30 March 2019 Schumer talk contribs created page Schumer lab: Important simulation tools (Created page with "==Coalescent simulations with macs== ==Admixture simulations with admix'em==")
- 18:16, 29 March 2019 Schumer talk contribs created page Schumer lab: Common file formats (Created page with "==Common file formats in genomics and the lab== ===General file formats=== ===Lab-specific file formats===")
- 16:03, 29 March 2019 Schumer talk contribs created page Schumer lab: Download data to Sherlock from box, dropbox or googledocs (Created page with "==rclone can download data to Sherlock== Super useful for convenience and especially for large files ===Download from box using rclone=== ===Download from dropbox using rcl...")
- 18:55, 26 March 2019 Schumer talk contribs created page Schumer lab: Primer design (Created page with "==Primer design== NCBI has a great tool for primer design called [https://www.ncbi.nlm.nih.gov/tools/primer-blast/ Primer BLAST]")
- 18:54, 26 March 2019 Schumer talk contribs created page Schumer lab: Submitting libraries for sequencing (Created page with "==Submitting libraries for sequencing==")
- 18:53, 26 March 2019 Schumer talk contribs created page Schumer lab: Pooling libraries for sequencing (Created page with "==Pooling samples for sequencing== First, double check that you have compatible indices. If you are pooling samples at equal ratios, use this file to calculate the dilution...")
- 18:38, 26 March 2019 Schumer talk contribs created page Schumer lab: Which indices should I use (Created page with "==General== ===Tn5 libraries=== ===RNAseq libraries=== ===Quail libraries===")
- 18:36, 26 March 2019 Schumer talk contribs created page Schumer lab: Which indices should I use? (Created page with "==General== ===Tn5 libraries=== ===RNAseq libraries=== ===Quail libraries===")
- 08:37, 26 March 2019 Schumer talk contribs created page Schumer lab: Pyrosequencing primer design (Created page with "Pyrosequencing primer design can be done through Pyromark, which is a PC-only program. Download Pyromark here: [cmgm.stanford.edu/pan/results/PYROSEQ/Software/PyroMarkAssayDe...")
- 08:30, 26 March 2019 Schumer talk contribs created page Schumer lab: Pyrosequencing at Stanford (Created page with "We perform pyrosequencing at the http://cmgm.stanford.edu/pan/section_html/PYRO/index.html PAN center on campus The contact for pyrosequencing is Alberto: alberto5@stanfo...")
- 08:26, 26 March 2019 Schumer talk contribs created page Schumer lab: Sanger Sequencing (Created page with "We do Sanger sequencing through the [http://cmgm.stanford.edu/pan/ PAN facility on campus]")
- 12:36, 25 March 2019 Schumer talk contribs created page Schumer lab:General (Created page with "*Building contacts *Lab member phone numbers are in box: Lab_contact_info.xls *Chemical waste pick up *Emergency")
- 12:21, 25 March 2019 Schumer talk contribs created page Schumer lab:Wet lab/Sequencing (Created page with "==Illumina sequencing resources== * Which indices should I use? ==Sanger sequencing resources== *Schumer lab: Primer design|...")
- 08:40, 25 March 2019 Schumer talk contribs created page Schumer lab: Where can I find commonly used files (Created page with "==Which genome assembly should I use==")
- 08:40, 25 March 2019 Schumer talk contribs created page Schumer lab: Where can I find commonly used files? (Created page with "==What genome assembly should I use?== ==What annotation file should I use?==")
- 08:21, 24 March 2019 Schumer talk contribs created page Schumer lab: slurm resources (Created page with "Here are some great slurm resources: 1. https://ulhpc-tutorials.readthedocs.io/en/latest/scheduling/advanced/ ULHPC guide")
- 05:49, 23 March 2019 Schumer talk contribs created page Talk:Schumer lab (Created page with "==Suggested sections to add==")
- 05:46, 23 March 2019 Schumer talk contribs created page Schumer lab:Fish room (Created page with "__FORCETOC__ ==Lab fish database== Find our lab specific fish database here: swordtails.zebrabase.org")
- 04:23, 17 January 2019 Schumer talk contribs created page Schumer lab: Sharing data with collaborators (Created page with "===Sharing data with collaborators=== We can share data with collaborators through our lab directory on oak and globus.")
- 16:23, 15 January 2019 Schumer talk contribs created page Schumer lab: Common errors (Created page with "This is a place to document common errors and how to fix them. Please add to it! __FORCETOC__ ==Common errors==")
- 18:56, 13 January 2019 Schumer talk contribs created page File:IlluminaParsing v1-2.pdf
- 18:56, 13 January 2019 Schumer talk contribs uploaded File:IlluminaParsing v1-2.pdf
- 21:30, 12 January 2019 Schumer talk contribs created page Schumer lab: Lab github (Created page with "==Lab github== Out lab GitHub is maintained here: https://github.com/Schumerlab On sherlock, our lab repositories are linked to our shared bin: <span style="font-family:Co...")
- 20:10, 12 January 2019 Schumer talk contribs created page Schumer lab: Useful one-liners (Created page with "==Samtools one-liners==")
- 13:57, 20 October 2018 Schumer talk contribs uploaded File:Website.jpg