https://osiris.eemb.ucsb.edu/wiki/galaxyucsb/index.php?action=history&feed=atom&title=Pull_sequences_from_old_454_assembly 2026-05-12T13:52:48Z Revision history for this page on the wiki MediaWiki 1.28.2 https://osiris.eemb.ucsb.edu/wiki/galaxyucsb/index.php?title=Pull_sequences_from_old_454_assembly&diff=19&oldid=prev 2011-11-11T00:58:56Z

<p>Created page with &quot;1. <a href="/wiki/galaxyucsb/index.php/Connect_to_macroevolution" title="Connect to macroevolution">Connect to macroevolution</a> using a terminal and ssh 2. Old 454 assemblies are in the directory /labdata/nfs/lab/454/projects/ type cd /labdata/nfs/lab/454/projects/ 3. Choo…&quot;</p> <p><b>New page</b></p><div>1. [[Connect to macroevolution]] using a terminal and ssh<br /> 2. Old 454 assemblies are in the directory /labdata/nfs/lab/454/projects/<br /> type cd /labdata/nfs/lab/454/projects/<br /> 3. Choose a project directory. You can list them by typing ls<br /> <br /> Some example projects as of 11-11-11<br /> <br /> Combined_Run_Portions TcMD_Aug10<br /> Cytherelloidea_californica TcMD_Tripedalia_cystophora_moredeveloped_planulalarvae<br /> Darwinula TEST<br /> ECE Tripedalia_planula<br /> Euphilomedes_chupacabra_CompoundEyesBoth Vargula_tsujii<br /> <br /> <br /> 4. cd to the &lt;Project directory&gt;<br /> <br /> 5. each project directory has a subdirectory called assembly<br /> cd assembly<br /> <br /> 6. Sequences are in a fasta file called lucy.seq because we use [[lucy]] to clean reads. Use a perl script to pull out the sequence of interest<br /> pull_seqs_by_name.pl lucy.seq &lt;seqeucne name to search for, like contig01772&gt;</div>

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