Coordinate format in text file for Juicer tools pre
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Robert Schöpflin
Apr 12, 2019, 2:53:22 PM4/12/19
to 3D Genomics
Dear group,
I was wondering, if the genomic coordinates (positions) in the textfile for the Juicer_tools-pre command are 0-based? From the behavior of Juicer_tools pre it seems to be 0-based. However, in the file merged_nodups.txt, which is produced by the Juicer-pipeline and which can be also used for the pre-command, I have the impression that the coordinates are 1-based. I did not find this information in the documentation. Sorry, if I have overlooked it in the wiki.
Best wishes
Robert
I was wondering, if the genomic coordinates (positions) in the textfile for the Juicer_tools-pre command are 0-based? From the behavior of Juicer_tools pre it seems to be 0-based. However, in the file merged_nodups.txt, which is produced by the Juicer-pipeline and which can be also used for the pre-command, I have the impression that the coordinates are 1-based. I did not find this information in the documentation. Sorry, if I have overlooked it in the wiki.
Best wishes
Robert
Neva Durand
Apr 13, 2019, 6:34:23 AM4/13/19
to Robert Schöpflin, 3D Genomics
Binning is done by dividing the position by the resolution. So reads 1-4999 will be in first 5kb bin, 5000-9999 in second, and so on. The position is given by BWA which is 1-based.
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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab
Robert Schöpflin
Apr 13, 2019, 10:00:22 AM4/13/19
to 3D Genomics
Dear Neva,
thanks for your response. Does it mean, that when having 5kb resolution that the first bin has a length of 4999 bp (1-4999), but all following bins have a length of 5000bp (5000-9999, ...)?
The intervals in the output of Juicer dump start at 0 (suggesting 0-based intervals), but if I understand correctly, they also refer to 1-4999, 5000-9999, because the coordinate of reads starts at 1.
It appears like having 1-based coordinates, but 0-based intervals. Would it be an alternative to make all bins the same length and use 1-based intervals from 1-5000, 5001-10000 (like displayed in Juicebox) or use 0-based coordinates instead and have 0-based intervals (0-4999, 5000-9999)?
Best wishes
Robert
thanks for your response. Does it mean, that when having 5kb resolution that the first bin has a length of 4999 bp (1-4999), but all following bins have a length of 5000bp (5000-9999, ...)?
The intervals in the output of Juicer dump start at 0 (suggesting 0-based intervals), but if I understand correctly, they also refer to 1-4999, 5000-9999, because the coordinate of reads starts at 1.
It appears like having 1-based coordinates, but 0-based intervals. Would it be an alternative to make all bins the same length and use 1-based intervals from 1-5000, 5001-10000 (like displayed in Juicebox) or use 0-based coordinates instead and have 0-based intervals (0-4999, 5000-9999)?
Best wishes
Robert
Neva Durand
Apr 13, 2019, 10:29:51 AM4/13/19
to Robert Schöpflin, 3D Genomics
I suppose there’s a slight discrepancy at the first bin but it doesn’t matter in practice, at least for human, due to the telomeres - the first possible read is at 10000.
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Robert Schöpflin
Apr 13, 2019, 3:01:23 PM4/13/19
to 3D Genomics
Dear Neva,
thanks for your response. I think in contigs of genome assemblies reads can also map to the first base. Additionally, the intervals of the bins are displayed in Juicebox as 1-5000, 5001-10000, ..., i.e. with an offset of 1 compared to how the binning is working.
I think using 0-based coordinates in the Juicer-Tool pre text files would solve these things:
(1) All bins would have the same size, going from 0-4999, 5000-9999, ... (0-based in Juicer tools and the hic-file)
(2) The intervals would fit to the notion in Juicebox (where bins are displayed in the one-based manner), the offset would disapear
Best wishes,
Robert
thanks for your response. I think in contigs of genome assemblies reads can also map to the first base. Additionally, the intervals of the bins are displayed in Juicebox as 1-5000, 5001-10000, ..., i.e. with an offset of 1 compared to how the binning is working.
I think using 0-based coordinates in the Juicer-Tool pre text files would solve these things:
(1) All bins would have the same size, going from 0-4999, 5000-9999, ... (0-based in Juicer tools and the hic-file)
(2) The intervals would fit to the notion in Juicebox (where bins are displayed in the one-based manner), the offset would disapear
Best wishes,
Robert
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