### Example CRAN Repository for Ubuntu 10.04 Source: http://qualimap.conesalab.org/doc_html/intro.html An example line to add to sources.list for installing R on Ubuntu 10.04 (Lucid) from a specific CRAN mirror. ```bash deb http://cran.stat.ucla.edu/bin/linux/ubuntu lucid/ ``` -------------------------------- ### Qualimap BAM QC Example Source: http://qualimap.conesalab.org/doc_html/command_line.html A basic example of how to run Qualimap BAM QC analysis. The output directory will be automatically created if not specified. ```bash qualimap bamqc -bam ERR089819.bam -c ``` -------------------------------- ### Run BamQC with Output Directory Source: http://qualimap.conesalab.org/doc_html/command_line.html Example of running the 'bamqc' tool and specifying an output directory for the HTML report and raw data. Ensure the input BAM file is correctly specified. ```bash qualimap bamqc -bam file.bam -outdir qualimap_results ``` -------------------------------- ### Run Qualimap from Installation Directory Source: http://qualimap.conesalab.org/doc_html/intro.html Execute the Qualimap application by running the provided script from its installation directory. This is the primary method for launching Qualimap on Unix-like systems. ```bash ./qualimap ``` -------------------------------- ### Example Qualimap RNA-seq Analysis Command Source: http://qualimap.conesalab.org/doc_html/command_line.html This is an example command to run RNA-seq QC analysis. It requires the input BAM file and GTF annotation file, and specifies an output directory. ```bash qualimap rnaseq -bam kidney.bam -gtf human.64.gtf -outdir rnaseq_qc_results ``` -------------------------------- ### Qualimap Counts QC Example Source: http://qualimap.conesalab.org/doc_html/command_line.html Example command to run Qualimap counts QC analysis. It specifies the input data file, enables comparison of conditions, sets the species to mouse, and defines the output directory. Ensure the input data file and counts file exist. ```bash qualimap counts -d GlcN_countsqc_input.txt -c -s mouse -outdir glcn_mice_counts ``` -------------------------------- ### Install OpenJDK 6 JRE on Ubuntu Source: http://qualimap.conesalab.org/doc_html/intro.html Install the OpenJDK 6 Java Runtime Environment on Ubuntu systems using the apt-get package manager. ```bash sudo apt-get install openjdk-6-jre ``` -------------------------------- ### Example Configuration File for Multi-sample BAM QC Source: http://qualimap.conesalab.org/doc_html/command_line.html Illustrates the format of the configuration file required by the -d argument. It specifies sample names, paths to BAM QC results or BAM files, and optionally sample conditions. ```text sample_1 sample_1_stats group_1 sample_2 sample_2_stats group_1 sample_3 sample_3_stats group_1 sample_4 sample_4_stats group_2 sample_5 sample_5_stats group_2 sample_6 sample_6_stats group_2 ``` -------------------------------- ### Install Required R Packages Dependencies Source: http://qualimap.conesalab.org/doc_html/intro.html Install system-level libraries required by some R packages used by Qualimap, such as libxml2-dev and libcurl4-openssl-dev. ```bash sudo apt-get install libxml2-dev sudo apt-get install libcurl4-openssl-dev ``` -------------------------------- ### Install Qualimap's R Dependencies using Script Source: http://qualimap.conesalab.org/doc_html/intro.html Execute the provided R script to automatically install all required R packages for Qualimap's advanced features. Ensure the QUALIMAP_HOME environment variable is set correctly. ```bash sudo Rscript $QUALIMAP_HOME/scripts/installDependencies.r ``` -------------------------------- ### Add CRAN Repository for R Installation on Ubuntu Source: http://qualimap.conesalab.org/doc_html/intro.html Add a CRAN mirror to the sources.list file to enable installation of the latest R version from public repositories on Ubuntu. Replace '' and '' with appropriate values. ```bash deb http:///bin/linux/ubuntu / ``` -------------------------------- ### Install Qualimap's R Dependencies Manually Source: http://qualimap.conesalab.org/doc_html/intro.html Install R packages required by Qualimap manually. This is an alternative to using the installation script. ```r install.packages("optparse") # From Bioconductor # source("http://bioconductor.org/biocLite.R") # biocLite(c("NOISeq", "Repitools", "Rsamtools", "GenomicFeatures", "rtracklayer")) ``` -------------------------------- ### Run BamQC with PDF Output File Source: http://qualimap.conesalab.org/doc_html/command_line.html Example demonstrating how to generate a PDF report for the 'bamqc' tool. The '-outfile' option specifies the name of the PDF report, while '-outdir' can still be used for raw data location. ```bash qualimap bamqc -bam file.bam -outfile result.pdf ``` -------------------------------- ### Run BamQC with Explicit PDF Output Format Source: http://qualimap.conesalab.org/doc_html/command_line.html Example showing how to explicitly set the output format to PDF using the '-outformat' option. The report will be saved in the specified output directory with a default name. ```bash qualimap bamqc -bam file.bam -outdir qualimap_results -outformat pdf ``` -------------------------------- ### Update Package List and Install R Core on Ubuntu Source: http://qualimap.conesalab.org/doc_html/intro.html After adding the CRAN repository, update the package list and install the R base core package on Ubuntu. ```bash sudo apt-get update sudo apt-get install r-base-core ``` -------------------------------- ### Import Public Key for CRAN Mirror Source: http://qualimap.conesalab.org/doc_html/intro.html Import the public key for a CRAN mirror if it's not already present, which is necessary for secure package installation on Ubuntu. ```bash gpg --keyserver subkeys.pgp.net --recv-key gpg -a --export | sudo apt-key add - ``` -------------------------------- ### Check R Version Source: http://qualimap.conesalab.org/doc_html/intro.html Verify the installed version of R using the Rscript command. Qualimap requires R version 3.1 or above. ```bash Rscript --version ``` -------------------------------- ### Running Qualimap Multi-BAMQC with a Configuration File Source: http://qualimap.conesalab.org/doc_html/command_line.html Demonstrates how to execute the qualimap multi-bamqc command using a specified input configuration file and output directory. Ensure the input file and directory exist. ```bash unzip gh2ax_chip_seq.zip cd gh2ax_chip_seq.txt qualimap multi-bamqc -i gh2ax_chip_seq.txt -outdir gh2ax_multibamqc ``` -------------------------------- ### Launch a QualiMap Tool Source: http://qualimap.conesalab.org/doc_html/command_line.html General command structure for launching any QualiMap analysis tool. Replace with the desired analysis (e.g., bamqc, rnaseq) and with specific parameters. ```bash qualimap ``` -------------------------------- ### Show Available QualiMap Tools Source: http://qualimap.conesalab.org/doc_html/command_line.html Use this command to list all available analysis tools within QualiMap and view their basic help information. ```bash qualimap --help ``` -------------------------------- ### Launch Qualimap on Windows Source: http://qualimap.conesalab.org/doc_html/intro.html Use the 'qualimap.bat' script to launch Qualimap on Microsoft Windows operating systems. ```bash qualimap.bat ``` -------------------------------- ### Qualimap multi-bamqc Command Usage Source: http://qualimap.conesalab.org/doc_html/command_line.html Displays the available options and arguments for the qualimap multi-bamqc command. Use this to understand the parameters for multi-sample BAM QC. ```bash usage: qualimap multi-bamqc [-c] -d [-gff ] [-hm ] [-nr ] [-nw ] [-outdir ] [-outfile ] [-outformat ] [-r] -c,--paint-chromosome-limits Only for -r mode. Paint chromosome limits inside charts -d,--data File describing the input data. Format of the file is a 2-column tab-delimited table. Column 1: sample name Column 2: either path to the BAM QC result or path to BAM file (-r mode) -gff,--feature-file Only for -r mode. Feature file with regions of interest in GFF/GTF or BED format -hm Only for -r mode. Minimum size for a homopolymer to be considered in indel analysis (default is 3) -nr Only for -r mode. Number of reads analyzed in a chunk (default is 1000) -nw Only for -r mode. Number of windows (default is 400) -outdir Output folder for HTML report and raw data. -outfile Output file for PDF report (default value is report.pdf). -outformat Format of the ouput report (PDF or HTML, default is HTML). -r,--run-bamqc Raw BAM files are provided as input. If this option is activated BAM QC process first will be run for each sample, then multi-sample analysis will be performed. ``` -------------------------------- ### Qualimap RNA-seq Command Line Usage Source: http://qualimap.conesalab.org/doc_html/command_line.html This displays the available options for the `qualimap rnaseq` command. Use this to understand parameter choices for RNA-seq QC analysis. ```bash usage: qualimap rnaseq [-a ] -bam -gtf [-oc ] [-outdir ] [-outfile ] [-outformat ] [-p ] -a,--algorithm Counting algorithm: uniquely-mapped-reads(default) or proportional. -bam Input mapping file in BAM format. -gtf Annotations file in Ensembl GTF format. -npb,--num-pr-bases Number of upstream/downstream nucleotide bases to compute 5'-3' bias (default is 100). -ntb,--num-tr-bias Number of top highly expressed transcripts to compute 5'-3' bias (default is 1000). -oc Path to output computed counts. -outdir Output folder for HTML report and raw data. -outfile Output file for PDF report (default value is report.pdf). -outformat Format of the ouput report (PDF or HTML, default is HTML). -p,--sequencing-protocol Sequencing library protocol: strand-specific-forward, strand-specific-reverse or non-strand-specific (default) -pe,--paired Setting this flag for paired-end experiments will result in counting fragments instead of reads. -s,--sorted This flag indicates that the input file is already sorted by name. If not set, additional sorting by name will be performed. Only required for paired-end analysis. ``` -------------------------------- ### Qualimap BAM QC Usage Source: http://qualimap.conesalab.org/doc_html/command_line.html This displays the usage information for the qualimap bamqc command, listing all available options and their descriptions. The -bam option is the only required parameter. ```bash usage: qualimap bamqc -bam [-c] [-gd ] [-gff ] [-hm ] [-nr ] [-nt ] [-nw ] [-oc ] [-os] [-outdir ] [-outfile ] [-outformat ] [-p ] -bam Input mapping file in BAM format -c,--paint-chromosome-limits Paint chromosome limits inside charts -cl,--cov-hist-lim Upstream limit for targeted per-bin coverage histogram (default is 50X) -dl,--dup-rate-lim Upstream limit for duplication rate historgram (default is 50) -gd,--genome-gc-distr Species to compare with genome GC distribution. Possible values: HUMAN or MOUSE. -gff,--feature-file Feature file with regions of interest in GFF/GTF or BED format -hm Minimum size for a homopolymer to be considered in indel analysis (default is 3) -ip,--collect-overlap-pairs Activate this option to collect statistics of overlapping paired-end reads -nr Number of reads analyzed in a chunk (default is 1000) -nt Number of threads (default is 8) -nw Number of windows (default is 400) -oc,--output-genome-coverage File to save per base non-zero coverage. Warning: large files are expected for large genomes -os,--outside-stats Report information for the regions outside those defined by feature-file (ignored when -gff option is not set) -outdir Output folder for HTML report and raw data. -outfile Output file for PDF report (default value is report.pdf). -outformat Format of the ouput report (PDF or HTML, default is HTML). -p,--sequencing-protocol Sequencing library protocol: strand-specific-forward, strand-specific-reverse or non-strand-specific (default) -sd,--skip-duplicated Activate this option to skip duplicate alignments from the analysis. If the duplicates are not flagged in BAM file, then they will be detected by Qualimap and can be selected for skipping. -sdmode,--skip-dup-mode Specific type of duplicated alignments to skip (if this option is activated). 0 : only flagged duplicates (default) 1 : only estimated by Qualimap 2 : both flagged and estimated ``` -------------------------------- ### Enable Headless Java Mode Source: http://qualimap.conesalab.org/doc_html/faq.html Disable the X11 display requirement for Java by setting the -Djava.awt.headless=true option. This can be done by modifying the java_options variable in the qualimap script or by setting the JAVA_OPTS environment variable. ```bash java_options="-Djava.awt.headless=true -Xmx$JAVA_MEM_SIZE -XX:MaxPermSize=1024m" ``` -------------------------------- ### Common QualiMap Command Line Options Source: http://qualimap.conesalab.org/doc_html/command_line.html These options are applicable to most QualiMap command line tools for configuring output. They control the output directory, PDF report filename, and report format. ```bash -outdir Output folder for HTML report and raw data. -outfile Output file for PDF report (default value is report.pdf). -outformat Format of the ouput report (PDF or HTML, default is HTML). ``` -------------------------------- ### Qualimap Counts QC Usage Source: http://qualimap.conesalab.org/doc_html/command_line.html Displays the usage information for the qualimap counts command, outlining available options and their descriptions. Use this to understand the parameters required for the analysis. ```bash usage: qualimap counts [-c] -d [-i ] [-k ] [-outdir ] [-outfile ] [-outformat ] [-R ] [-s ] -c,--compare Perform comparison of conditions. Currently 2 maximum is possible. -d,--data File describing the input data. Format of the file is a 4 column tab-delimited table. Column 1: sample name Column 2: condition of the sample Column 3: path to the counts data for the sample Column 4: index of the column with counts -i,--info Path to info file containing genes GC-content, length and type. -k,--threshold Threshold for the number of counts -outdir Output folder for HTML report and raw data. -outfile Output file for PDF report (default value is report.pdf). -outformat Format of the ouput report (PDF or HTML, default is HTML). -R,--rscriptpath Path to Rscript executable (by default it is assumed to be available from system $PATH) -s,--species Use built-in info file for the given species: HUMAN or MOUSE. ``` -------------------------------- ### Unset DISPLAY Environment Variable Source: http://qualimap.conesalab.org/doc_html/faq.html If encountering 'Can't connect to X11 window server' errors, unset the DISPLAY environment variable to allow Qualimap to run without a graphical display. ```bash unset DISPLAY ``` ```bash export DISPLAY=:0 ``` -------------------------------- ### Qualimap Clustering Command Usage Source: http://qualimap.conesalab.org/doc_html/command_line.html Use this command to perform clustering of epigenomic signals. Specify sample BAM files, control BAM files, and a regions file. ```bash usage: qualimap clustering [-b ] [-c ] -control [-expr ] [-f ] [-l ] [-name ] [-outdir ] [-outformat ] [-r ] -regions -sample [-viz ] -b,--bin-size size of the bin (default is 100) -c,--clusters comma-separated list of cluster sizes -control comma-separated list of control BAM files -expr name of the experiment -f,--fragment-length smoothing length of a fragment -l upstream offset (default is 2000) -name comma-separated names of the replicates -outdir output folder -outformat output report format (PDF or HTML, default is HTML) -r downstream offset (default is 500) -regions path to regions file -sample comma-separated list of sample BAM files -viz visualization type: heatmap or line ``` ```bash qualimap clustering -sample clustering/hmeDIP.bam -control clustering/input.bam -regions annotations/transcripts.human.64.bed -outdir clustering_result ``` -------------------------------- ### Qualimap Compute Counts Command Usage Source: http://qualimap.conesalab.org/doc_html/command_line.html Use this command to compute counts from mapping data. Requires a BAM file and a GTF/GFF/BED file. ```bash usage: qualimap comp-counts [-a ] -bam -gtf [-id ] [-out ] [-p ] [-pe] [-s ] [-type ] -a,--algorithm Counting algorithm: uniquely-mapped-reads(default) or proportional -bam Mapping file in BAM format -gtf Region file in GTF, GFF or BED format. If GTF format is provided, counting is based on attributes, otherwise based on feature name -id GTF-specific. Attribute of the GTF to be used as feature ID. Regions with the same ID will be aggregated as part of the same feature. Default: gene_id. -out Path to output file -p,--sequencing-protocol Sequencing library protocol: strand-specific-forward, strand-specific-reverse or non-strand-specific (default) -pe,--paired Setting this flag for paired-end experiments will result in counting fragments instead of reads -s,--sorted This flag indicates that the input file is already sorted by name. If not set, additional sorting by name will be performed. Only required for paired-end analysis. -type GTF-specific. Value of the third column of the GTF considered for counting. Other types will be ignored. Default: exon ``` ```bash qualimap comp-counts -bam kidney.bam -gtf ../annotations/human.64.gtf -out kidney.counts ``` -------------------------------- ### Set Java Heap Memory Size Source: http://qualimap.conesalab.org/doc_html/faq.html Increase the maximum Java heap memory size for Qualimap using the --java-mem-size argument. Ensure there is no whitespace between the argument and its value. ```bash qualimap --java-mem-size=1200M ``` ```bash qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G ``` -------------------------------- ### Modify Default Java Memory Size Source: http://qualimap.conesalab.org/doc_html/faq.html Change the default Java memory size by editing the JAVA_MEM_DEFAULT_SIZE variable in the Qualimap launching script. ```bash JAVA_MEM_DEFAULT_SIZE=”1200M” ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.