Chromatin accessibility associated with aquaculture relevant traits in Nile tilapia - Data applicable to the study

#################################################

## We provide data relevant to the publication, summarised as:

# 1. BED file of O. niloticus CNE annotations

# 2. Annotated gill peaks

# 3. Overlap of annotated gill peaks with SNPs

# 4. Gene promoter TFBS footprints with gill SNP-peaks

#################################################

### 1. O. niloticus (Nile tilapia) annotated CNEs

## File: Oreochromis_niloticus.UMD_NMBU.CNE.annot.bed

## Columns are:

# 1. CNE chromosome/scaffold

# 2. CNE start

# 3. CNE end

# 4. CNE type: Average_Conservation Score >=0.9 = hCNE; aCNE = Average_Conservation Score <0.9, deviating from the neutral model, and so have a negative CONACC score, lnl ratio <0.05, and significant divergence (altsubscale >1)

# 5. CNE score (all = .)

# 6. CNE strand

# 7. closest Ensembl Gene ID

# 8. Ensembl Transcript ID (all = .)

# 9. CNE details - Total conservation score (PhastCons); length of CNE; Average_Conservation Score (PhastCons); Gene distance from CNE

# 10. closest gene symbol

#################################################

### 2. Collated replicate gill open chromatin peaks intersected with annotation features - all IDR true and false peaks provided

## File: On_G_ATAC_peaks.collated.narrowPeak.features.gff

## Columns are:

# 1: peak chromosome/scaffold

# 2: peak ID

# 3: peak feature

# 4: peak start

# 5: peak end

# 6: peak score

# 7: peak strand

# 8. feature frame

# 9: peak calling details from MACS2 (; separated)

  # a. signal value - measurement of overall enrichment for the region

  # b. p-val - stat significance (-log10)

  # c. q-val - stat significance using FDR (-log10)

  # d. peak - point-source called for this peak; 0-based offset from chromStart (like the peak summit)

  # e. IDR - true or false for reproducibility between replicates

  # f. ensemblID for gene promoter

  # g. gene symbol

#################################################

### 3. Collated replicate gill open chromatin peaks annotated by feature and intersected with tilapia SNPs

## File: On_G_ATAC_peaks.collated.narrowPeak.features.intersectSNPs.bed

## Columns are:

# 1: SNP chromosome/scaffold

# 2: SNP start

# 3: SNP end

# 4: SNP ID

# 5: SNP score

# 6: SNP strand

# 7: SNP feature (all '5kb_gene_promoter')

# 8: SNP gene annotation (from GTF)

# 9: peak chr

# 10: peak start

# 11: peak end

# 12: peak ID

# 13: peak score

# 14: peak strand

# 15: peak feature

# 16: peak calling details from MACS2 (; separated)

  # a. signal value - measurement of overall enrichment for the region

  # b. p-val - stat significance (-log10)

  # c. q-val - stat significance using FDR (-log10)

  # d. peak - point-source called for this peak; 0-based offset from chromStart (like the peak summit)

  # e. IDR - true or false for reproducibility between replicates

  # f. ensemblID for gene promoter

  # g. gene symbol

#################################################

### 4. Gene promoter TFBS footprints with gill SNP-peaks (from collated replicate peaks - all IDR true and false peaks provided)

## File: On_G_ATAC_mpbs_GenePromfpSNPATAC.txt

## Columns are:

# 1: SNP chromosome/scaffold

# 2: SNP start

# 3: SNP end

# 4: SNP ID

# 5: SNP score

# 6: SNP strand

# 7: SNP feature (all '5kb_gene_promoter')

# 8: SNP gene annotation (from GTF?)

# 9: peak chromosome/scaffold

# 10: peak start

# 11: peak end

# 12: peak ID

# 13: peak score

# 14: peak strand

# 15: peak feature (all '5kb_gene_promoter')

# 16: peak calling details from MACS2 (; separated)

  # a. signal value - measurement of overall enrichment for the region

  # b. p-val - stat significance (-log10)

  # c. q-val - stat significance using FDR (-log10)

  # d. peak - point-source called for this peak; 0-based offset from chromStart (like the peak summit)

  # e. IDR - true or false

  # f. ensemblID for gene promoter

  # g. gene symbol

# 17: presence/absence - all present

# 18: TFBS chromosome/scaffold

# 19: TFBS start

# 20: TFBS end

# 21: TFBS ID

# 22: bit-score of motif match

# 23: TFBS strand

# 24: footprint chr

# 25: footprint start

# 26: footprint end

# 27: footprint ID

# 28: footprint tag count (TC)

# 29: footprint strand - all are .

# 30: TFBS and footprint overlap