Search Results for: MV-NIS

Unfortunately, file names for gene expression counts data from recount2 are very generic (like what we see in the example_rna_seq_counts directory). Thus, we would like to rename these files to make them Read More...

The mv command can also be used to move a folder to another. To demonstrate this, make a copy of the folder lesson3 and call it lesson3_copy. cp -r lesson3 lesson3_copy Move lesson3_ Read More...

The mv command can also be used to move a folder to another. To demonstrate this, make a copy of the folder lesson3 and call it lesson3_copy. cp -r lesson3 lesson3_copy Move lesson3_ Read More...

pwd (print working directory) ls (list) nano (basic editor for creating small text files) rm (remove files) mkdir (make a directory) cd (change directory) mv (rename or move files) less (view files) man (manual) cp ( Read More...

We will create an alias for this command. sort | uniq -c | sort -rn The "sort" utility sorts text and binary files by lines. The "uniq" utility reads input, compares adjacent lines Read More...

Move the file counts.csv to lesson3 using the mv command, where the arguments are item to move (ie. the file counts.csv) destination (ie. the folder lesson3) mv counts.csv lesson3 List the contents Read More...

We can also use the mv command to rename folders. To see this let's make a copy of the lesson4 folder called lesson4_new. Again, we need to append -r to the cp command Read More...

Next, we will create a new folder called new_house. mkdir new_house Then we will move lesson4_copy_1 to the folder new_house. Moving a folder to another only works when the name of Read More...

Rename text1.txt to text_file1.txt. {{Sdet}}{{Ssum}}Solution{{Esum}} mv text1.txt text_file1.txt {{Edet}}

Following import, we want to check our sequence quality and the number of sequences per sample (read depth). This can be done using qiime demux summarize . qiime demux summarize \ --i-data demuxsequences.qza \ --o-visualization demuxsequences-summary.qzv Read More...

This is similar to mv but will create an actual copy of a file. You will need to specify what you are copying (the source) and where you want to make the copy (the target). Read More...

As with any language, the learning curve for Unix can be quite steep. However, to get started analyzing data you really need to understand the following: Directory navigation: what the directory tree is, how to Read More...

As with any language, the learning curve for Unix can be quite steap. However, to get started analyzing data you really need to understand the following: Directory navigation: what the directory tree is, how to Read More...

The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command line. Begin Read More...

Lesson 2 Practice The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command Read More...

pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the "rm" command to remove files. Be careful! mkdir (make a directory) and Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the "rm" command to remove files. Be careful! mkdir (make a directory) and Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

After the merged expression counts table has been created, we can proceed with differential expression analysis. Let's use DESeq2 again for this. But first, let's move counts.csv (the merged salmon expression table) Read More...

As with any language, the learning curve for Unix can be quite steep. However, to work on Biowulf you really need to understand the following: Directory navigation: what the directory tree is, how to navigate Read More...

touch creates an empty file nano basic editor for creating small text files rm remove files or directories. Be careful! mkdir make a directory and rmdir (remove a directory with NO files) mv rename or Read More...

To work on Biowulf you really need to understand the following: Directory navigation: what the directory tree is, how to navigate and move around with cd Absolute and relative paths: how to access files located Read More...

All of the files in the alignment output folder have "hcc1395_" prepended. To make these files easier to work with, this exercise will remove the "hcc1395" from these files using the Read More...

Let's now change into the lesson4 folder and list its contents. cd lesson4 ls Indeed, we see that the two files now reside in the lesson4 folder. counts_copy.csv text_1_copy.txt Let' Read More...

cat hcc1395_sample_ids.txt | parallel "bowtie2 -x references/22 -1 reads/{}_R1.fq -2 reads/{}_R2.fq -S hcc1395_bowtie2/{}.sam" Change into hcc1395_bowtie2 and remove hcc1395 from the SAM alignment outputs. Read More...

Rename results.csv to deg_results.csv. mv results.csv deg_results.csv

Rename results.csv to deg_results.csv. mv results.csv deg_results.csv

mkdir: make new directory mv: move or rename file or directory rm: delete sinteractive: request an interactive session head: view content at the beginning of a file tail: view content at the end of a Read More...

mkdir: make new directory mv: move or rename file or directory rm: delete sinteractive: request an interactive session head: view content at the beginning of a file tail: view content at the end of a Read More...

cp (to copy files or directories) mv (to move/rename files or directories) rm (to remove/delete files or directories) rmdir (to remove empty directory) tree (to view directory tree)

In the previous lesson, we learned to move, rename, and remove files as well as directories in Unix. Commands that we learned include mv (to move or rename file or directories) tree (to generate a Read More...

Stay in the srr1553423_fastqc folder. Copy SRR1553606_fastqc.sh from /data/classes/BTEP/unix_on_biowulf_2023_documents/SRR1553606_fastqc to the srr1553423_fastqc folder. Change the file name to SRR1553423_fastqc.sh. {{Sdet}}{{Ssum}} Read More...

The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command line. Begin Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the "rm" command to remove files. Be careful! mkdir (make a directory) and Read More...

pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

This is similar to mv but will create an actual copy of a file. You will need to specify what you are copying (the source) and where you want to make the copy (the target). Read More...

The Biopharmaceutical Development Program (BDP) provides resources for the development of investigational biological agents. The BDP supports feasibility through development and Phase I/II cGMP manufacturing plus regulatory documentation.The BDP was established in 1993. We Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment. conda activate bioinfo The jellyfish program is dependent on a program called "gcc" which is Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Lesson 2: Navigating file systems with Unix Quick review Unix is an operating system We use a unix shell (typically bash) to run many bioinformatics programs We need to learn unix to use non-GUI based tools Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * cd * mkdir * curl * tar * cat * grep * wc * outputting data * piping data from one command to another * cut Learn: * du * pip * csvkit * datamash Read More...

Bioinformatics Training and Education Program 15 January – 15 February 2023 BTEP Bulletin Contact us at ncibtep@nih.gov FEATURED BIOINFORMATICS EVENTS Data Management Sharing: Part 1 and Part 2 DOE-NCI Collaboration: MOSSAIC for Advancing Computational Models for Cancer Research Variation Read More...

As with any language, the learning curve for Unix can be quite steep. However, to work on Biowulf you really need to understand the following: Navigating the File System: Understanding the hierarchical structure of directories, Read More...

As with any language, the learning curve for Unix can be quite steep. However, to work on Biowulf you really need to understand the following: Navigating the File System: Understanding the hierarchical structure of directories, Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

ssh (connect to remote computer such as a high performance computing cluster) pwd (print working directory) cd (change directory) ls (list directory content) mkdir (make a directory) and rmdir (remove a directory, must be empty Read More...

ssh (connect to remote computer such as a high performance computing cluster) pwd (print working directory) cd (change directory) ls (list directory content) mkdir (make a directory) touch (creates an empty file) nano (basic editor Read More...

For these practice questions, check the present working directory and if needed, change into the /data/username folder (username is the student account ID). What command is used to check present working directory? {{Sdet}}{{Ssum}} Read More...

For these practice questions, check the present working directory and if needed, change into the /data/username folder (username is the student account ID). What command is used to check present working directory? {{Sdet}}{{Ssum}} Read More...

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

Lesson 1: Introduction to Unix and the Shell Lesson Objectives Review the course syllabus and general structure of lessons to come. Introduce Unix and describe how it differs from other operating systems. Introduce and get set Read More...

Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...

Lesson 1: Introduction to Unix and the Shell Lesson Objectives Course overview. Introduce Unix and describe how it differs from other operating systems. Introduce and get set up on DNAnexus and the GOLD system. Discuss ways Read More...

Lesson 16: RNA sequencing review and classification based analysis Before getting started, remember to be signed on to the DNAnexus GOLD environment. Review In the previous classes, we learned about the steps involved in RNA sequencing Read More...

Lesson 1: Introduction to Biowulf, Unix, and R Learning Objectives Learn about why you may want to use R on Biowulf. Refresh Unix and R skills. This lesson will not be hands on. Why use R Read More...

Learning Objectives Understand the components of an HPC system. How does this compare to your local desktop? Learn about Biowulf, the NIH HPC cluster. Learn about the command line interface and resources for learning. What Read More...

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