Merge pull request #24 from VIB-PSB/feature/icres-based-grns

Making the iCREs files public with download instructions

README.md

@@ -54,7 +54,7 @@ The pipeline will run in parallel for multiple ACR BED input files. The two opti
   For maize RefGen_v5
   ```
   wget https://zenodo.org/record/8386283/files/zma_v5_genome_wide_motif_mappings.bed?download=1 -O data/zma_v5/zma_v5_genome_wide_motif_mappings.bed
-  wget https://zenodo.org/record/8386283/files/zma_v5_locus_based_motif_mappings_5kbup_1kbdown.bed?download=1 data/zma_v5/ -O zma_v5_locus_based_motif_mappings_5kbup_1kbdown.bed
+  wget https://zenodo.org/record/8386283/files/zma_v5_locus_based_motif_mappings_5kbup_1kbdown.bed?download=1 data/zma_v5/ -O data/zma_v5/zma_v5_locus_based_motif_mappings_5kbup_1kbdown.bed
   ```
 
 NOTE: MINI-AC was developed using the following versions: Nextflow version 21.10.6, Singularity version 3.8.7-1.el7 and in a Sun Grid Engine (SGE) computer cluster.
@@ -69,17 +69,25 @@ nextflow -C mini_ac.config run mini_ac.nf --mode <genome_wide|locus_based> --spe
 
 Having problems running MINI-AC? Check the [FAQ](docs/FAQ.md).
 
-## iCREs-based MINI-AC [NOT AVAILABLE UNTIL PUBLICATION]
+## iCREs-based MINI-AC
 
 Given the amount of resources available to profile regulatory DNA in maize, we curated a collection of integrated cis-regulatory elements (iCREs) by combining and comparing different CRE-profiling methods (details to be published).
 
 We implemented a new framework in which it is possible to run MINI-AC given a list of maize genes. It works by retrieving the genomic coordinates of the iCREs associated with genes of interest, and submitting them to motif enrichment and GRN inference using the genome-wide mode of MINI-AC. iCREs-based MINI-AC can only be run for maize, and not for Arabidopsis. In addition, we offer different sets of iCREs that are used in the run: the "maxF1" (`maxf1`) set or the "all" (`all`) set. The first uses a set of putative CREs that is smaller but more precise (less false positives), while the second uses a more comprehensive and complete collection of maize putative CREs.
 
 To download files with the genomic coordinates of the iCREs, the following commands should be executed on the **top-level directory of the repository**:
 
-```shell
-NOT AVAILABLE UNTIL PUBLICATION
-```
+  For maize RefGen_v4
+  ```
+  wget https://zenodo.org/records/13143829/files/maxf1_icres_zma_v4.bed?download=1 -O data/icres/maxf1_icres_zma_v4.bed
+  wget https://zenodo.org/records/13143829/files/all_icres_zma_v4.bed?download=1 -O data/icres/all_icres_zma_v4.bed
+  ```
+  For maize RefGen_v5
+  ```
+  wget https://zenodo.org/records/11192739/files/maxf1_icres_zma_v5.bed?download=1 -O data/icres/maxf1_icres_zma_v5.bed
+  wget https://zenodo.org/records/11192739/files/all_icres_zma_v5.bed?download=1 -O data/icres/all_icres_zma_v5.bed
+  ```
+
 
 To run iCREs-based MINI-AC, the [configuration file](./mini_ac_icres.config) should be prepared as explained [here](./docs/pipeline_configuration.md). Only two parameters change in comparison to the regular MINI-AC runs. Instead of providing a BED file with ACR genomic coordinates, a list of gene IDs from the maize genome version V4 or V5 should be provided, as exemplified [here](./example/inputs/gene_set_files/UP_gene_set.txt). In addition, an iCREs set should be specified (`maxf1` or `all`). Next, the following Nextflow command should be executed: