Package 'pasillaBamSubset'

Title: Subset of BAM files from "Pasilla" experiment
Description: Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped.
Authors: Hervé Pagès
Maintainer: Hervé Pagès <[email protected]>
License: LGPL
Version: 0.51.0
Built: 2026-10-10 10:31:10 UTC
Source: https://github.com/bioc/pasillaBamSubset

Help Index

Utilities returning the paths to BAM files untreated1_chr4.bam and untreated3_chr4.bam

Description

BAM file untreated1_chr4.bam contains the subset of untreated1.bam (single-end reads, "Pasilla" experiment) where only alignments located on chr4 (Fly) were kept.

BAM file untreated3_chr4.bam contains the subset of untreated3.bam (paired-end reads, "Pasilla" experiment) where only alignments located on chr4 (Fly) were kept.

FASTA file dm3_chr4.fa contains the full sequence of the D. melanogaster chromosome 4.

untreated1_chr4, untreated3_chr4 and chr4 return the path to those files.

Usage

untreated1_chr4()
untreated3_chr4()
dm3_chr4()

Details

See the pasilla data package for details about the "Pasilla" experiment (RNA-seq, Fly).

BAM files untreated1.bam and untreated3.bam contain single-end and paired-end reads aligned to reference genome BDGP Release 5 (aka the dm3 genome on the UCSC Genome Browser).

Fasta file dm3_chr4.fa from UCSC, the Apr. 2006 assembly of the D. melanogaster genome (dm3, BDGP Release 5): DNA sequence for fly chromosome 4.

Examples

untreated1_chr4()
untreated3_chr4()
dm3_chr4()