Computational protocol: The chromatin remodeling complex Swi/Snf regulates splicing of meiotic transcripts in Saccharomyces cerevisiae

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Protocol publication

[…] Chromatin immunoprecipitation (ChIP)-seq reads () were obtained (GEO accession number GSE61210) and converted to FastQ format using the NCBI SRA Toolkit. Bowtie2 was used to align FastQ reads to SacCer3 with only one reported alignment (−k 1). Genomic track files from immunoprecipitation and input alignments were created using SAMTools, BEDTools and the UCSC bedgraphToBigWig utility. After normalizing input and immunoprecipitation pileup tracks for differential read count, a ratio track was created by dividing the normalized immunoprecipitation track by the normalized input track. Pileup ratios of the region 500+/− of the Translation Start Site (TSS) of genes of interest were retrieved and were added coordinate-wise to generate a 500+/− association array for each list of genes. Association array values were normalized for the number of genes included and vertically scaled between 0 and 100 to generate the meta-association array. […]

Pipeline specifications

Software tools Bowtie2, SAMtools, BEDTools, GATK
Databases SRA
Application ChIP-seq analysis