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Fig. 3 | BMC Bioinformatics

Fig. 3

From: ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS

Fig. 3

Workflow of the automatic pipeline for the analysis of ChIP-seq data in MARACAS. The maracas-chip-seq pipeline receives as input a parameter file specifying the microalga of interest, the execution mode (sequential or parallel), the fastq files locations or SRA (sequence read archive) accession numbers and the type of protein-DNA interaction under study either transcription factors or histone modifications. After data acquisition in fastq format, sequence quality analysis is performed using fastqc. Read mapping to the reference genome is performed using bowtie2 and is stored in BAM format. A synchronization point ensuring the completion of all replicates processing is necessary before carrying out peak calling with macs2. Reports in html and pdf format are generated with details on sequence quality analysis and mapping process. These reports include links to download the identified peaks in BED format and the genome wide mapping signal in bigwig format. These outputs are compatible with the input formats for AlgaeFUN in order to facilitate further annotation and visualization of the identified genomic loci significantly bound or occupied by the transcription factor or histone modification of interest

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