Pull sequences from old 454 assembly

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1. Connect to macroevolution 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. Choose a project directory. You can list them by typing ls

Some example projects as of 11-11-11

Combined_Run_Portions TcMD_Aug10 Cytherelloidea_californica TcMD_Tripedalia_cystophora_moredeveloped_planulalarvae Darwinula TEST ECE Tripedalia_planula Euphilomedes_chupacabra_CompoundEyesBoth Vargula_tsujii


4. cd to the <Project directory>

5. each project directory has a subdirectory called assembly cd assembly

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 pull_seqs_by_name.pl lucy.seq <seqeucne name to search for, like contig01772>

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