Only necessary if outformat = 'SAM' as header always included in 'BAM'.īoolean. Skip alignments with MAPQ smaller than this value.īoolean. Include output of alignments with anyīits set in this value present in the FLAG field. Text file where each line contains the reference name in the first column Generated automatically from the existing header. Interest or regions defined in the format 'RNAME:START'. Vector of characters specifying the path to sorted BAM files.Įither path to a single BED file containing regions of Suffix to add to the basename of the file e.g, _psort (forīoolean. String specifying maximum memory per thread suffix K/M/Gīoolean. Run_samview this should be SAM or 'BAM' only.Ī positive integer specifying the number of sorting and String specifying output format: ('SAM'/'BAM'/'CRAM'). The path to samtools (if not in executable path). Run_samsort ( file = NULL, samtools = 'samtools', outformat = 'BAM', threads = 1, memory = '768M', sortbyname = FALSE, suffix = '', keep = TRUE ) run_samindex ( samtools = 'samtools', bamfile = NULL, threads = 1 ) run_samview ( samtools = 'samtools', file = NULL, regions = NULL, chrom.sizes = NULL, include.flag = NULL, exclude.flag = NULL, minQual = NULL, outformat = NULL, outname = NULL, include.header = FALSE, count = FALSE, threads = 1, subsample = NULL, keep.paired = TRUE, = TRUE, remove.unmapped = FALSE, = FALSE, remove.duplicates = FALSE, = FALSE, remove.mitochondrial = NULL ) run_samflagstat ( samtools = 'samtools', threads = 1, bamfile = NULL )Ī vector of characters specifying the path to the bam files. run_samsort: Wrapper scripts for SAMtools functions.run_sambambadup: Mark duplicates in BAM file.run_homer: Run HOMER for promoter motif enrichment.run_hisat2: Wrapper script to run HISAT2.run_goseq: Gene ontology and pathway analysis of DE genes.run_diff: Run the differential analysis pipeline.read_multifastqc: Read a a directory of FastQC data files.read_fastqc: Read a single FastQC data file.

process_counts: Pre-processing of counts.

make_venn: Make venn diagrams showing overlapping gene lists.

make_bigwig: Create bigwig files from BAM.

load_samples: Load sample metadata file.

limma_pipe: Pipeline for limma+voom analysis.

edger_pipe: Pipeline for edgeR analysis.

edger_norm: Count normalisation using edgeR.

deseq2_pipe: Pipeline for DESeq2 analysis.

deseq2_norm: Count normalisation using DESeq2.

create_se: Create Summarized Experiment.

create_pca: Create principal component analysis plot from DDS object.

create_mds: Create multi-dimensional scaling plot from DGE object.

create_hmp: Heatmap of most differential genes.

create_contrast: Design and contrast matrices.

count_reads: Count reads in bam files using featureCounts.

annotation: SAF file for human hg19 genome.

aggregate_fqc: Aggregate and summarise FastQC reports for multiple samples.

Samtools threads