This is a public collection of documentation about ChIP-seq and ChIP-Rx pipelines used by the PNDS (Plant Nuclear Dynamics & Signaling) Team led by Clara Bourbousse & Fredy Barneche.

Scripts and documentation by Adrien Vidal.

Step-by-step guides to genomic analysis pipelines used by the team.

ChIP-Seq pipeline

ChIP-Rx pipeline

Scripts used in the above guides.

bedFromFasta.pl: Perl script. Creates a .bed table of the full length of the sequences from a .fasta file.

bedFromGff.pl: Perl Script. Creates a .bed table of the regions from a .gff file. With the possibility to specify which tag contains the ID, to filter by feature type and to enforce ID uniqueness.

mergeOverlappingRegions.sh: Bash script. Uses a comination of bedtools functions to search for overlaps of the genomic regions of the between two files and generate merged regions bed file out of selected regions.

Genomic resources used by the the team when applying the above pipelines to Arabidopsis thaliana experiments.

Reference genomes:

• ⇗TAIR10_chr_all.fas.gz: Arabidopsis thaliana TAIR10 genome assembly.
• ⇗Col-CEN_v1.2.fasta.gz: Arabidopsis thaliana Col-CEN genome assembly.
• ⇗Download page for Arabidopsis thaliana Col-CC genome assembly.
• ⇗Download page for Drosophila melanogaster release 6 genome assembly.

Annotation:

• Araport11_GFF3.gene.201606.bed: Araport 11 annotation for genes on Arabidopsis thaliana TAIR10 genome assembly as a .bed file. Converted from the june 2016 annotation.
• Araport11_GFF3.TAIR10.transposable_element.201606.bed: Araport 11 annotation for transposable elements on Arabidopsis thaliana TAIR10 genome assembly. Converted from the june 2016 annotation.
• Col-CEN_v1.2_genes.araport11.gene.bed: Lifted Araport 11 annotation for genes on Arabidopsis thaliana Col-CEN genome assembly. Converted from the .gff3 annotation.

Blacklists:

• TAIR10_blacklist.bed: A blacklist of aberrant regions for the Arabidopsis thaliana TAIR10 genome.
• Col-CEN_blacklist.bed: A blacklist of aberrant regions for the Arabidopsis thaliana Col-CEN genome.