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This is a small project to make the anvi'o interactive interface able to give the user the opportunity to work with Hi-C data (more information on this technology is [here](https://en.wikipedia.org/wi…
meren updated
5 years ago
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Hi
I tried to scaffold my contig level genome with my hic data but failed with the segmentation fault error.
I think this error can be occurred due to the large hic alignment, which is about 700Gb…
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Hi, thank you for the powerful script.
Now, I have the haplotype-resolved contig-level assemblies, but I don't have the child Hi-C. I have only the Hi-C data of this sample. Can I use this script to …
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Hey Nicholas,
Wonderful pipeline -- I appreciate the added NextFlow implementation.
I had a request/recommendation that may improve compatibility with promoter-capture Hi-C users: a utility scr…
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I am trying to plot TADs I called on a Hi-C matrix with resolution 1kb. But no contacts are being plotted on the map. This is my command:
`hicPlotTADs --tracks tracks.ini --region chr01:6800000-85000…
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I have PACBIO SMRT Sequel data - and both Hi-C and Chicago Illumina data - but no standard PE or matepair Illumina data. Would you recommend using NextPolish with just the PacBio data - or would it b…
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Hi! If I have created a modified reference genome by introducing additional chromosomes that are, for instance, translocations between chr1 and chr12, is it possible to simulate Hi-C data using just t…
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Hello, @malonge
I tried to merge my 3 scaffolds obtained by command "ragtag.py scaffold" using corrected fasta.
Bam file of the hic was attached with the index.
And, that command was below.
rag…
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Hi Olga,
I am trying to use the supp/make-rainbow-tracks-assembly.sh script to make tracks.bedpe file to visualise the chromogram (similar to Fig 1 from Dudchenko et al 2017). I have couple of poin…
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Hi, Thanks for your software. I ran SALSA but unfortunately I didn't have satisfying result.
I applied the Arima mapping pipeline and got this statistics before SALSA:
```
perl $STATS $REP_DIR…