All epigenetic data used in the FIRE publication is available on AWS as a public dataset at the following URL:
Results are organized at the top level by sample, e.g.:
The structure of the results within each of these folders is then uniform with the following important files (using GM12878 as the example sample):
| File | Description |
|---|---|
| GM12878/FDR-peaks/FDR-FIRE-peaks.bed.gz | FIRE peaks called at FDR 0.05 |
| GM12878/FDR-peaks/FDR.track.bed.gz | FIRE coverage and FDR values for the whole genome |
| GM12878/hap1-vs-hap2/FIRE.hap.differences.bed | Differences in FIRE peaks between haplotypes |
| GM12878/fiber-calls/FIRE.bed.gz | Individual FIREs called from single molecule fiber-seq data |
| GM12878/trackHub/hub.txt | Track hub for visualizing all the FIRE results in the UCSC genome browser |
Description of columns you will find in the FDR FIRE peaks file:
| Column | Description |
|---|---|
| #chrom | Chromosome of the peak |
| peak_start | Start of the peak |
| peak_end | End of the peak |
| start | Start of the maximum of the peak |
| end | End of the maximum of the peak |
| coverage | Coverage of the peak |
| fire_coverage | Coverage of the FIREs in the peak |
| score | FIRE score of the peak |
| *{H1,H2} | Repeats of previous columns but specific for each of the two haplotypes |
| FDR | False discovery rate of the peak |
| log_FDR | -10*log10 of the FDR |
| FIRE_size_mean | Mean size of the FIREs in the peak |
| FIRE_size_ssd | Standard deviation of the size of the FIREs in the peak |
| FIRE_start_ssd | Standard deviation of the start of the FIREs in the peak |
| FIRE_end_ssd | Standard deviation of the end of the FIREs in the peak |
| pass_coverage | Whether the peak passes coverage filters |
We include UCSC trackHubs for each sample at the following URL and we also have a description of the trackHub here:
| Sample | Track hub URL |
|---|---|
| GM12878 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/GM12878/trackHub/hub.txt |
| 30X_GM12878 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/30X_GM12878/trackHub/hub.txt |
| K562-PS00075 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/K562-PS00075/trackHub/hub.txt |
| PS00338_COLO829BL_1 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00338_COLO829BL_1/trackHub/hub.txt |
| PS00356_COLO829BL_2 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00356_COLO829BL_2/trackHub/hub.txt |
| COLO_T_2_PS00_418_451_488 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/COLO_T_2_PS00_418_451_488/trackHub/hub.txt |
| PS00272 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00272/trackHub/hub.txt |
| PS00321 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00321/trackHub/hub.txt |
| PS00327 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00327/trackHub/hub.txt |
| PS00381 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00381/trackHub/hub.txt |
| PS00382 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00382/trackHub/hub.txt |
| PS00383 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00383/trackHub/hub.txt |
| PS00384 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00384/trackHub/hub.txt |
| PS00389 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00389/trackHub/hub.txt |
| PS00392 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00392/trackHub/hub.txt |
| PS00404 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00404/trackHub/hub.txt |
| PS00422 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00422/trackHub/hub.txt |
| PS00456 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00456/trackHub/hub.txt |
| PS00459 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00459/trackHub/hub.txt |
| PS00465 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00465/trackHub/hub.txt |
| PS00468 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00468/trackHub/hub.txt |
| PS00471 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00471/trackHub/hub.txt |
| PS00476 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00476/trackHub/hub.txt |
| PS00479 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00479/trackHub/hub.txt |
| PS00482 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00482/trackHub/hub.txt |
| PS00485 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/PS00485/trackHub/hub.txt |
| ST001-liver | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/ST001-liver/trackHub/hub.txt |
| ST001-lung | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/ST001-lung/trackHub/hub.txt |
| UDN318336_PS00189 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/UDN318336_PS00189/trackHub/hub.txt |
| UDN633333_PS00115 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/UDN633333_PS00115/trackHub/hub.txt |
| HG002 | https://s3-us-west-1.amazonaws.com/stergachis-manuscript-data/2024/Vollger_et_al/FIRE/HG002/trackHub/hub.txt |