Changes between Version 33 and Version 34 of FAQ

Timestamp:

09/02/25 09:39:33 (6 weeks ago)

Author:

gbell

Comment:

--

FAQ

@@ -221 +221 @@
      * nt                         => 2.9
 1. [=#tophat_bowtie How do I run '''tophat/bowtie on the LSF with a gzip'd tar (*.tar.gz)''' file?]
-  * 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)"
+  * sbatch --partition=20 --job-name=tophat--mem=32G --wrap "tophat ... <(tar xvzfO ...) <(tar xvzfO ...)", this is using process substitution 
+    * 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)"
 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.