Changes between Version 34 and Version 35 of FAQ


Ignore:
Timestamp:
02/02/26 14:14:41 (12 days ago)
Author:
gbell
Comment:

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  • FAQ

    v34 v35  
    36361. 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]]
    37371. Why do I get '''[#wi_ncbi_blast different BLAST results]'''  from [[http://fry.wi.mit.edu/blast/ | WI]] and NCBI Blast? [[br]] [[br]]
    38 1. How do I run '''[#tophat_bowtie tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)]''' file?  [[br]] [[br]]
     381. How do I run '''[#tophat_bowtie tophat/bowtie on the cluster with a gzip'd tar (*.tar.gz)]''' file?  [[br]] [[br]]
    39391. How can I run '''[#alphafold AlphaFold 2.0-2.3]''' here at Whitehead?  [[br]] [[br]]
    40401. How can I run '''[#alphafold3 AlphaFold 3]''' here at Whitehead?  [[br]] [[br]]
    … …  
    109109   * 'wrap' means that 'sbatch will wrap the specified command string in a simple "sh" shell script, and submit that script to the slurm controller'.
    110110
    111    * See [https://clusterguide.wi.mit.edu/using-the-slurm-cluster/ IT's Using the slurm cluster] for sample commands, changes in the environment (compared to the older LSF cluster) and links to more documentation
     111   * See [https://clusterguide.wi.mit.edu/using-the-slurm-cluster/ IT's Using the slurm cluster] for sample commands and links to more documentation
    112112   [[br]] [[br]]
    1131131. [=#perlR How can I find out what '''Perl modules or R packages''' are installed?] Which version is currently installed in the server? [[br]] [[br]]
    … …  
    220220     * all RefSeq sequences       => 0.47
    221221     * nt                         => 2.9
    222 1. [=#tophat_bowtie How do I run '''tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)''' file?]
     2221. [=#tophat_bowtie How do I run '''tophat/bowtie on the cluster with a gzip'd tar (*.tar.gz)''' file?]
    223223  * sbatch --partition=20 --job-name=tophat--mem=32G --wrap "tophat ... <(tar xvzfO ...) <(tar xvzfO ...)", this is using process substitution
    224224    * eg. sbatch --partition=20 --job-name=tophat--mem=32G --wrap "tophat -p 10 -g 1 -o mapped_data_SRR905147_unique -N 2 -I 10000 --segment-length 25 --segment-mismatches 2 hg19 <(tar xvzfO s_2_1_sequence.txt.tar.gz ACTTGA-s_2_1_sequence.txt) <(tar xvzfO CAGATC-s_2_1_sequence.txt.tar.gz CAGATC-s_2_1_sequence.txt)"