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How many files and directories are in the lesson3_practice folder? {{Sdet}}{{Ssum}}Solution{{Esum}} ls -l drwxr-x--- 2 wuz8 wuz8 4096 Jan 18 21:34 sample_sequence_data -rw-r----- 1 wuz8 wuz8 46 Jan 18 21:34 text1.txt One director and one file. {{ Read More...
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There are instructions for running SRA-Toolkit on Biowulf here ([https://hpc.nih.gov/apps/sratoolkit.html])(https://hpc.nih.gov/apps/sratoolkit.html). To start with, we will start up an interactive node using the & Read More...
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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...
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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...
Frederick, MD
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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...
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05/03/2023 - Partek Flow is your start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with analyzing Read More...
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sessionInfo() R version 4.4.0 (2024-04-24) Platform: aarch64-apple-darwin20 Running under: macOS Sonoma 14.7.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/ Read More...
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The Molecular Signatures Database (MSigDB) is a curated resource of thousands of gene sets by the Broad Institute. These sets were curated for use with GSEA software but are used with other tools as well. Read More...
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The command below will subset the expression counts for the RABL2B gene. hbr_uhr_chr22_counts[hbr_uhr_chr22_counts["Geneid"]=="RABL2B"] Geneid HBR_1.bam HBR_2.bam HBR_3.bam Read More...
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These questions can be answered in excel. However, the data would need to be reshaped. To see what I mean, let's take a brief look at the data in Excel. Notice that there are Read More...
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sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur ... 10.16 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/ Read More...
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05/16/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...
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In comma separated files the columns are separated by commas and the rows are separated by new lines. To read comma separated files, we can use the specific functions ?read.csv() and ?read_csv() . Let' Read More...
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For the following plots, let's use the diamonds data ( ?diamonds ). The diamonds dataset comes in ggplot2 and contains information about ~54,000 diamonds, including the price, carat, color, clarity, and cut of each diamond. --- R4 Read More...
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How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR Read More...
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The SRA (Sequence Read Archive) at NCBI is a large, public database of DNA sequencing data. The repository holds "short reads" generated by high-throughput next-generation sequencing, usually less than 1,000 bp. We will download Read More...
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Let's now take a look at our final differential analysis results table (results_with_gene_names_labeled.txt), using the SLC2A11 gene as an example and below we use the column command to Read More...
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fastq-dump and fasterq-dump can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. fastq-dump SRR1553607 creates the file: SRR1553607.fastq Check the file to make Read More...
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fastq-dump and fasterq-dump can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. fastq-dump SRR1553607 creates the file: SRR1553607.fastq Check the file to make Read More...
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Once we have done this, we can activate renv within our project. But, first, let's verify the location of our renv cache. R renv::paths$cache() # Check the cache location renv::init(bioconductor = "3.16& Read More...
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To subset a column of a pandas dataframe, the bracket notation followed by the column name can be used. For instance, to extract the Geneid column in hbr_uhr_chr22_counts do the following. hbr_ Read More...
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In comma separated files the columns are separated by commas and the rows are separated by new lines. To read comma separated files, we can use the specific functions ?read.csv() and ?read_csv(). Let' Read More...
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Panda's loc function allows for subsetting by row or column names. For instance, to retrieve the Geneid column, do the following. The ":" denotes get every row. hbr_uhr_chr22_counts.loc[:,['Geneid']] Read More...
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Panda's loc function allows for subsetting by row or column names. For instance, to retrieve the gene id column, do the following. The ":" denotes get every row. hbr_uhr_chr22_counts.loc[:,[' Read More...
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Q1. Let's use some functions. a. Use sum() to add the numbers from 1 to 10. Q1a: Solution sum(1:10) ## [1] 55 b. Compute the base 10 logarithm of the elements in the following vector and save to an Read More...
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Help Session Lesson 4 Plotting with ggplot2 For the following plots, let's use the diamonds data ( ?diamonds ). The diamonds dataset comes in ggplot2 and contains information about ~54,000 diamonds, including the price, carat, color, clarity, and Read More...
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Data import and reshape Objectives 1. Learn to import multiple data types 2. Data reshape with tidyr : pivot_longer() , pivot_wider() , separate() , and unite() Installing and loading packages So far we have only worked with objects that Read More...
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This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: using trimmomatic to remove low-quality bases from a sequence Always remember to activate the bioinformatics environment. conda activate bioinfo We will be Read More...
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Bioinformatics
This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: using trimmomatic to remove low-quality bases from a sequence Always remember to activate the bioinformatics environment. conda activate bioinfo We will be Read More...
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This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * downloading data from SRA * decompressing tar files * e-utilities * fastq-dump Learn: * sra-stat * XML format * automating SRA downloads * working with comma-separated values (csv) format * Read More...
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Before we can align the HBR and UHR raw sequencing data to human chromosome 22 transcriptome, we need to create an index of this transcriptome (like we did with the genome). This will make the alignment Read More...
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Lesson 6: sra-tools, e-utilities, and parallel This page uses some content directly from the Biostar Handbook by Istvan Albert. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch or swarm Read More...
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Lesson 6: Downloading data from the SRA For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch Read More...
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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...
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Lesson 3: R Project Management and renv Learning objectives Discuss the importance of reproducibility Learn ways to make R analyses more reproducible Learn how to set up and organize an R project Learn how to use Read More...
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fastq-dump and fasterq-dump are modules in the SRA Toolkit and can be used to download FASTQ-formatted data. Both download the data in SRA format and convert it to FASTQ format. If working on a high Read More...
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For tabular data in the form of csv files, which could contain multiple columns, the columns do not print to the terminal nicely aligned. The column command can fix this. The options and arguments in Read More...
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Changes to a coding project (including scripts, data, and other content) should be saved periodically, similar to clicking on the "save" button to periodically save changes when constructing a word document. This is Read More...