Bioconductor read in fasta file

A character vector giving the directory path relative or absolute or single file name of FASTA files to be read. The grep -style pattern describing file names to be read. The default character 0 results in attempted input of all files in the directory.

Additional arguments used by methods or, for writeFasta , writeXStringSet. There is no guarantee of order in which files are read. The function returns, invisibly, the length of object , and hence the number of records written. There is a writeFasta method for any class derived from ShortRead. For more information on customizing the embed code, read Embedding Snippets. Such genomic ranges are very useful for describing both data e. GRanges is an object representing a vector of genomic locations and associated annotations.

Each element in the vector is comprised of a sequence name, a range, a strand, and optional metadata e. Use help to list the help pages in the GenomicRanges package, and vignettes to view and access available vignettes. These operations are useful both in data analysis e.

Biostrings classes e. In the example below we will construct a DNAString and show some manipulations. The sequences in the file can be read in using getSeq from the Biostrings package. ShortRead package from Bioconductor can be used for working with fastq files.

Here we illustrate a quick example where one can read in multiple fasta files, collect some statistics and generate a report about the same. BiocParallel is another package from Bioconductor which parallelizes this task and speeds up the process. The GenomicAlignments package is used to input reads aligned to a reference genome.

In this next example, we will read in a BAM file and specifically read in reads supporting an apparent exon splice junction spanning position of chromosome The package RNAseqData.

Basics Bioconductor packages are listed on the biocViews page. Visit this landing page, and note the description, authors, and installation instructions. Packages are often written up in the scientific literature, and if available the corresponding citation is present on the landing page. Also on the landing page are links to the vignettes and reference manual and, at the bottom, an indication of cross-platform availability and download statistics.

GRanges Domain-specific analysis — explore the landing pages, vignettes, and reference manuals of two or three of the following packages. Important packages for analysis of differential expression include edgeR and DESeq2 ; both have excellent vignettes for exploration. What other ChIP-seq packages are listed on the biocViews page?

Several packages identify copy number variants from sequence data, including cn. The CNTools package provides some useful facilities for comparison of segments across samples. Microbiome and metagenomic analysis is facilitated by packages such as phyloseq and metagenomeSeq. Metabolomics, chemoinformatics, image analysis, and many other high-throughput analysis domains are also represented in Bioconductor; explore these via biocViews and title searches.

The Biostrings package is used to represent DNA and other sequences, with many convenient sequence-related functions. Check out the functions documented on the help page? Also check out the BSgenome package for working with whole genome sequences, e. See for instance the? Check out the? Explore the ShortRead vignette and Scalable Genomics labs to see approaches to effectively processing the large files.