Zcat uncompresses the file and | ‘pipes’ the uncompressed file to head which prints the first 20 lines View the first 20 lines, using zcat to unzip zcat Sample1_R1.fastq.gz | head -n 20 Question: Why are there two files for each sample? We have called these sample 1-3 for simplicity. This is to allow you to complete the workshop in a reasonable time, and to avoid you having to sit around waiting for up to 30 minutes for some of the computational steps to complete. Note, that these files only contain 10% of the original amount of sequence data. TriTrypDB-39_LdonovaniBPK282A1_Genome.fastaĪ fasta format file containing the Leishmania infantum reference genomeĪlso, six fastq.gz files that are the paired-end Illumina sequence reads from three parasite isolates from Ethiopia: Sample1_R1.fastq.gz You can list the directory contents sorted by date (-t, newest first), together with details such as file size (-l, long format): ls -lt You will need to cd into this directory to see its contents. This will create a directory called workshop2_files. This means the current directory, and can be put in place of the full path for the directory we want to copy our files toĭecompress the file tar zxvf workshop2_ NB: Note the space between workshop2_ and the dot. To copy this file to your scratch directory, do this: cp /opt/yarcc/data/biology/mbiol_sequence_analysis_2019/workshop2_. This is stored in the directory /opt/yarcc/data/biology/mbiol_sequence_analysis_2019. The files you need for this workshop are bundled in a gzipped ‘tar’ file, called workshop2_ Files you make will appear hereĬopy over the relevant data to this new directory using the cp command using the following format cp /path/to/files /destination/path You are now ‘in’ or working from this directory. In this second window, go to your scratch space and make a working directory with a sensible name ( avoid using spaces in file and directory names), and move into this directory: cd /scratch/username So, open a second connection to your designated server (using putty). You can have several terminal windows (connections to your server) running at the same time. To display the processes you are running on your server, type: top -u username It is useful to be able to keep track of whether your jobs are completed or still running. If your username is in the alphabetic range jdh562 to xc1051, you will have you run your analysis for the workshops (and your projects) on a different server called .uk. If your userid is in the alphabetic range ag1314 to ja1082, you can run the analysis for the workshops (and your projects) on the server called .uk Make sure you have logged into the server before you continue. You will use this file to keep your notes. If you are working on this from outside the University you will have to use the York VPN through the Pulse Secure application.įirst thing: Using Notepad (or another text editor) make a plain text file on your computer called something sensible such as MBiol_Sequence_Analysis_workshop2_notes.txt The analyses will be carried out on the linux operating system.įollow the steps to log in to the .uk server as detailed in the Introduction to linux and serversĪs you are working on this within the University you can use putty (from a PC) or a terminal window (from a Mac).
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