Changes between Version 22 and Version 23 of FAQ

Timestamp:

05/19/23 16:36:49 (20 months ago)

Author:

twhitfie

Comment:

--

FAQ

@@ -37 +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]]
 1. How do I run '''[#tophat_bowtie tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)]''' file?  [[br]] [[br]]
-1. How can I run '''[#alphafold AlphaFold 2.0-2.2]''' here at Whitehead?  [[br]] [[br]]
+1. How can I run '''[#alphafold AlphaFold 2.0-2.3]''' here at Whitehead?  [[br]] [[br]]
 1. How can I output '''[#pvalues small p-values]''' from R?  [[br]] [[br]]
 ----
@@ -209 +209 @@
   * bsub bash -c "tophat ... <(tar xvzfO ...) <(tar xvzfO ...)", this is using process substitution 
     * eg. bsub bash -c "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)"
-1. [=#alphafold How can I run '''AlphaFold 2.2''' here at Whitehead?]
+1. [=#alphafold How can I run '''AlphaFold 2.3''' here at Whitehead?]
   * You'll need access to a system with a GPU, or the new GPU queue.  IT can help you choose and obtain access to GPU systems if required.
   * For a working command to be executed on fry.wi.mit.edu, which then sends the AlphaFold command to the GPU node on the slurm cluster, see /nfs/BaRC_Public/BaRC_code/shell/run_AlphaFold/Commands.sh
@@ -217 +217 @@
 sbatch -J AF220_1 --export=ALL,FASTA_NAME=Sample_protein_1.fa,USERNAME=myUsername,FASTA_PATH=proteins,AF2_WORK_DIR=/nfs/BaRC_Public/BaRC_code/shell/run_AlphaFold ./RunAlphaFold_2.2.0_slurm.sh
 
-sbatch -J AFmult --export=ALL,FASTA_NAME=Leucine_zipper_minimal.fa,USERNAME=myUsername,FASTA_PATH=proteins,AF2_WORK_DIR=/nfs/BaRC_Public/BaRC_code/shell/run_AlphaFold ./RunAlphaFold_multimer_2.2.0_slurm.sh
+sbatch -J AFmult --export=ALL,FASTA_NAME=Leucine_zipper_minimal.fa,USERNAME=myUsername,FASTA_PATH=proteins,AF2_WORK_DIR=/nfs/BaRC_Public/BaRC_code/shell/run_AlphaFold ./RunAlphaFold_multimer_2.3.0_slurm.sh
 }}}
     where the inputs are