Changes between Version 31 and Version 32 of FAQ
- Timestamp:
- 06/26/24 13:55:28 (6 months ago)
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FAQ
v31 v32 15 15 1. How can I '''[#LSF submit a job to the LSF cluster]'''?[[br]] [[br]] 16 16 1. How can I find out what '''[#perlR Perl modules or R packages]''' are installed? Which version is currently installed in the server?[[br]] [[br]] 17 1. How can I '''[#xwindow connect to tak]'''?[[br]] [[br]]17 1. How can I '''[#xwindow connect to fry]'''?[[br]] [[br]] 18 18 1. How can I '''[#servers get to my or my lab shared storage]'''?[[br]] [[br]] 19 19 1. Where can I '''[#blast find local BLAST databases]'''?[[br]] [[br]] … … 25 25 1. Where can I '''[#UCSCmirror find the local mirror of the UCSC genome browser]'''?[[br]] [[br]] 26 26 1. Where can I '''[#galaxy find the local mirror of Galaxy]'''?[[br]] [[br]] 27 1. Where can I '''[#rstudio find R Studio on tak]'''?[[br]] [[br]]27 1. Where can I '''[#rstudio find a local R Studio server]'''?[[br]] [[br]] 28 28 1. Where can I '''[#IGV find IGV download]'''?[[br]] [[br]] 29 29 1. Which software should I use to '''[#heatmaps cluster, create and display heatmaps]'''? [[br]] [[br]] … … 35 35 1. How do I '''[#R_pkg_install install an R package locally]'''?[[br]] [[br]] 36 36 1. I need to '''[#transfer send/receive very large data files]''' to/from a colleague outside of Whitehead. What is the best way to do this?[[br]] [[br]] 37 1. Why do I get '''[#wi_ncbi_blast different BLAST results]''' from [[http:// tak.wi.mit.edu/blast/ | WI]] and NCBI Blast? [[br]] [[br]]37 1. Why do I get '''[#wi_ncbi_blast different BLAST results]''' from [[http://fry.wi.mit.edu/blast/ | WI]] and NCBI Blast? [[br]] [[br]] 38 38 1. How do I run '''[#tophat_bowtie tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)]''' file? [[br]] [[br]] 39 39 1. How can I run '''[#alphafold AlphaFold 2.0-2.3]''' here at Whitehead? [[br]] [[br]] … … 53 53 * Use **blast2seq** [https://blast.ncbi.nlm.nih.gov/Blast.cgi?BLAST_SPEC=blast2seq&LINK_LOC=align2seq&PAGE_TYPE=BlastSearch] for a quick local alignment [[br]] [[br]] 54 54 1. [=#blat How can I '''run BLAT locally'''?] [[br]] [[br]] 55 * See our [http://bioinfo.wi.mit.edu/bio/bioinfo/docs/blat_tak.html Using BLAT on tak] page.[[br]] [[br]]55 * See our [http://bioinfo.wi.mit.edu/bio/bioinfo/docs/blat_tak.html Using BLAT on fry] page.[[br]] [[br]] 56 56 1. [=#promoter How can I '''get the promoter sequence''' of a gene?] [[br]] [[br]] 57 57 - Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Bioinformatics] genome browser. … … 68 68 1. [=#entrez How can I '''access the Whitehead version of the Entrez Gene database'''?] [[br]] [[br]] 69 69 * Whitehead BaRC designed a local copy of the Entrez Gene database using MySQL 70 * You need a MySQL client to access the database, either a desktop tool like [http://wb.mysql.com/ MySQL Workbench] or a takaccount.70 * You need a MySQL client to access the database, either a desktop tool like [http://wb.mysql.com/ MySQL Workbench] or a fry account. 71 71 * The information you need: 72 72 * Hostname = devo.wi.mit.edu … … 74 74 * username = barc_read_only 75 75 * password = Ask BaRC about this 76 * On tak, use the command76 * On fry, use the command 77 77 * mysql -u barc_read_only -h devo.wi.mit.edu -D entrez_gene -p[[br]] [[br]] 78 78 1. [=#hottopics How can I find slides and materials from '''past Hot Topics talks'''?] [[br]] [[br]] … … 107 107 * With either system, double click on the icon to get the "command prompt", the window in which you can type commands. 108 108 * Windows only: After opening Cygwin, start X Windows by typing "startx". A new terminal window will open, and you should use that one. 109 * From the command prompt, connect to tak(or another Unix/Linux computer) with a command like109 * From the command prompt, connect to fry (or another Unix/Linux computer) with a command like 110 110 {{{ 111 ssh username@ tak.wi.mit.edu -Y111 ssh username@fry.wi.mit.edu -Y 112 112 or 113 ssh username@ tak.wi.mit.edu -X114 where username is the name of your takaccount.113 ssh username@fry.wi.mit.edu -X 114 where username is the name of your fry account. 115 115 You'll be prompted for your password. 116 116 }}} … … 128 128 * See [http://it.wi.mit.edu/systems/file-storage/lab-share-paths lab share paths] to get to your lab storage area. [[br]] [[br]] 129 129 1. [=#blast Where can I '''find local BLAST databases'''?] [[br]] [[br]] 130 * BLAST formated databases can be found in /nfs/seq/Data on tak.[[BR]][[br]]130 * BLAST formated databases can be found in /nfs/seq/Data on fry.[[BR]][[br]] 131 131 1. [=#genomeSeqs Where can I '''find genome sequences'''? ] [[br]] [[br]] 132 * Genome sequences can be found in /nfs/genomes on tak.[[BR]][[br]]132 * Genome sequences can be found in /nfs/genomes on fry.[[BR]][[br]] 133 133 1. [=#btFormats Where can I '''find genomes formatted for bowtie, tophat, or blat'''?] [[br]] [[br]] 134 134 * Within many directories on /nfs/genomes you can these additional files.[[BR]][[br]] … … 145 145 1. [=#galaxy Where can I '''find the local mirror of Galaxy'''?][[br]] [[br]] 146 146 * It used to be at [https://galaxy.wi.mit.edu/] but we no longer provide Galaxy. [[br]] [[br]] 147 1. [=#rstudio Where can I '''find R Studio on tak'''?][[br]] [[br]]147 1. [=#rstudio Where can I '''find a local R Studio server'''?][[br]] [[br]] 148 148 * [https://rstudio.wi.mit.edu] [[br]] [[br]] 149 149 1. [=#IGV Where can I '''find IGV download'''?] [[br]] [[br]] … … 199 199 1. [=#transfer I need to '''send/receive very large data files''' to/from a colleague outside of Whitehead. What is the best way to do this?] 200 200 * Our IT department has built two tools to help you share large files with your colleagues. [Sendit for files up to 2GB; Vort for files over 2GB http://wi-inside.wi.mit.edu/departments/it/services/filetransfer] [[br]] [[br]] 201 1. [=#wi_ncbi_blast Why do I get '''different BLAST results''' from http:// tak.wi.mit.edu/blast/ and NCBI Blast?]201 1. [=#wi_ncbi_blast Why do I get '''different BLAST results''' from http://fry.wi.mit.edu/blast/ and NCBI Blast?] 202 202 * WI and NCBI pages have very different defaults. As a result, a hit at WI with an e-value of 1e-12 but at NCBI the alignment is completely different and leads to an e-value of 2e-98. 203 203 * Word sizes are different, as are match/mismatch scores (1/-3 at WI, 2/-3 at NCBI).
