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Hello!
I am wondering if you run Juicer to produce the duplicate-free list of paired alignment with default parameters, or if you went for more stringent alignment parameters, like "only perfect matc…
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Hi,
Thank you for inventing this amazing tool :)
Recently, I have been working with the salmon genome to build the 3D chromosome from Hi-C without LADs.
(Hi-C library was generated from live…
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Hi, I have been trying to use 3D-function "3DMax-3Dmodeler" in the Genomeflow to visualize my hic data. I know that the input file requires a contact matrix in sparse matrix format. I was using hic-s…
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Thank you for supplying Chrom3D!
I am currently working on the 3D reconstruction of the full genome of a human cell line (male, mostly in interphase) from unphased HiC data.
I was wondering if the…
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Dear Olga,
I have now tried different parameters on my dataset. I started with a chromosome-level assembly built from linkage map. The default parameters severely degraded this assembly, which alr…
melop updated
4 years ago
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Hi
We assembled a genome with hifiasm (typical commands in hic mode) and divided the chromosomes with hic reads. However, we found that some contigs are not covered by hic reads. More complicated i…
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hello Sir, I was analyzing repeat masker output for Oryza_sativa_HR12, was faced the following error, please suggest a solution. Should I share RMasker output file?
> Oryza_sativa_HR12_aggregated
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### Description of the bug
I get "Java heap space" error for any configuration of Nextflow versions even though I have added "NXF_OPTS='-Xms1g -Xmx4g'" to my .bashrc...
N E X T F L O W ~ version…
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Hi, I finished an assembly and the result is:
Type Length (bp) Count (#)
N10 22880485 3
N20 10335838 10
N30 …
cj2jy updated
5 months ago
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Dear Professor.
I found a error when evaluating with the heatmap`ALLHiC_plot`, now I want to try flipping them, but I don't know their location and ctg id. How can I know their information and change…