CTCF BED file with orientation
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Muhammad Shamim
Nov 30, 2016, 6:48:33 PM11/30/16
to 3D Genomics
Hi Berkley,
Apologies for the late response.
If you want all CTCF motifs, we have FIMO results hosted at https://bcm.app.box.com/v/juicerawsmirror/
under /opt/juicer/references/genomewide_ctcf_motif_fimo
If you're looking for an oriented CTCF track for a custom map, we'll upload some scripts to the github repo.
Best,
- Muhammad S Shamim
Suhas Rao
Nov 30, 2016, 8:36:07 PM11/30/16
to 3D Genomics
Hi Berkley,
The link that Muhammad provided has files that contain all reasonable matches to the CTCF motif genomewide, keep in mind that the vast majority of these are not actually bound by CTCF in any given cell type.
If you're looking for motif calls for the loop anchors we annotated in Rao, Huntley, et al Cell 2014, you can find those on GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525). All the files named *HiCCUPS_looplist_with_motifs.txt.gz have motif information for the anchors where the motif could be identified or inferred. Details about the file format are provided in the README file (GSE63525_OVERALL_README.rtf). Details about the methods used to identify the motifs are provided in Section VI.e.7 and Section VI.e.8 of the Extended Experimental Procedures of Rao, Huntley, et al. (Cell 2014). Note that our most recent Juicer implementation of the motif identification algorithm, we switched from using STORM for motif identification to using FIMO, as described in Section II.d. of the Supplemental Experimental Procedures of Durand, Shamim, et al (Cell Systems 2016). All other details remain as described in Rao, Huntley et al.
If you specifically want oriented motifs for CTCF ChIP-Seq peaks found in GM12878, I've attached a BED file. These motifs were identified as described in Section VI.e.7 of Rao, Huntley et al. The underlying CTCF ChIP-Seq data is from ENCODE and is outlined in Table S3 of Rao, Huntley et al. If you want to make similar tracks for other CTCF ChIP-Seq data sets, as Muhammad mentioned, we will be uploading some scripts to github.
Please let me know if you have any questions.
Cheers,
Suhas
The link that Muhammad provided has files that contain all reasonable matches to the CTCF motif genomewide, keep in mind that the vast majority of these are not actually bound by CTCF in any given cell type.
If you're looking for motif calls for the loop anchors we annotated in Rao, Huntley, et al Cell 2014, you can find those on GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525). All the files named *HiCCUPS_looplist_with_motifs.txt.gz have motif information for the anchors where the motif could be identified or inferred. Details about the file format are provided in the README file (GSE63525_OVERALL_README.rtf). Details about the methods used to identify the motifs are provided in Section VI.e.7 and Section VI.e.8 of the Extended Experimental Procedures of Rao, Huntley, et al. (Cell 2014). Note that our most recent Juicer implementation of the motif identification algorithm, we switched from using STORM for motif identification to using FIMO, as described in Section II.d. of the Supplemental Experimental Procedures of Durand, Shamim, et al (Cell Systems 2016). All other details remain as described in Rao, Huntley et al.
If you specifically want oriented motifs for CTCF ChIP-Seq peaks found in GM12878, I've attached a BED file. These motifs were identified as described in Section VI.e.7 of Rao, Huntley et al. The underlying CTCF ChIP-Seq data is from ENCODE and is outlined in Table S3 of Rao, Huntley et al. If you want to make similar tracks for other CTCF ChIP-Seq data sets, as Muhammad mentioned, we will be uploading some scripts to github.
Please let me know if you have any questions.
Cheers,
Suhas
Berkley Gryder
Dec 2, 2016, 10:10:46 AM12/2/16
to 3D Genomics
Hi Muhammad and Suhas,
Thanks! These are extemely helpful! For the file which has all the CTCF motifs, I would of course filter to obtain only the ones that overlap with CTCF ChIP-seq peaks in my own cell line's data.
All the best!
Berkley
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